From 2b6e86cc7f6d10e6bc6b77284b3e38e6b9db2db7 Mon Sep 17 00:00:00 2001
From: fridellsa <gus.fridell@nih.gov>
Date: Wed, 12 Jan 2022 16:28:23 -0500
Subject: [PATCH 01/91] Changed library loading location before config
---
workflows/rnaseq/downstream/rnaseq.Rmd | 21 +++++++++++++++++++++
1 file changed, 21 insertions(+)
diff --git a/workflows/rnaseq/downstream/rnaseq.Rmd b/workflows/rnaseq/downstream/rnaseq.Rmd
index 8bce54f6..a36dd080 100644
--- a/workflows/rnaseq/downstream/rnaseq.Rmd
+++ b/workflows/rnaseq/downstream/rnaseq.Rmd
@@ -26,6 +26,27 @@ devtools::document('../../../lib/lcdbwf')
devtools::load_all('../../../lib/lcdbwf')
```
+```{r}
+library(AnnotationHub)
+library(BiocParallel)
+library(clusterProfiler)
+library(cowplot)
+library(DESeq2)
+library(dplyr)
+library(DT)
+library(genefilter)
+library(ggplot2)
+library(gridExtra)
+library(plotly)
+library(purrr)
+library(ReactomePA)
+library(readr)
+library(reshape)
+library(tibble)
+library(tximport)
+library(UpSetR)
+```
+
```{r config}
# HOW TO CONFIGURE ------------------------------------------------------
From b9bcb65e9793df97858166223628a6e63c28346c Mon Sep 17 00:00:00 2001
From: fridells51 <63575426+fridells51@users.noreply.github.com>
Date: Mon, 24 Jan 2022 10:12:03 -0500
Subject: [PATCH 02/91] Update rnaseq.Rmd
---
workflows/rnaseq/downstream/rnaseq.Rmd | 24 +-----------------------
1 file changed, 1 insertion(+), 23 deletions(-)
diff --git a/workflows/rnaseq/downstream/rnaseq.Rmd b/workflows/rnaseq/downstream/rnaseq.Rmd
index 05981028..02fd620d 100644
--- a/workflows/rnaseq/downstream/rnaseq.Rmd
+++ b/workflows/rnaseq/downstream/rnaseq.Rmd
@@ -27,7 +27,7 @@ devtools::document('../../../lib/lcdbwf')
devtools::load_all('../../../lib/lcdbwf')
```
-```{r}
+```{r libraries}
library(AnnotationHub)
library(BiocParallel)
library(clusterProfiler)
@@ -82,28 +82,6 @@ if (config$parallel$parallel){
Last run: `r date()`
-```{r libraries}
-library(AnnotationHub)
-library(BiocParallel)
-library(clusterProfiler)
-library(cowplot)
-library(DESeq2)
-library(dplyr)
-library(DT)
-library(genefilter)
-library(ggplot2)
-library(gridExtra)
-library(plotly)
-library(purrr)
-library(ReactomePA)
-library(readr)
-library(reshape)
-library(tibble)
-library(tximport)
-library(UpSetR)
-```
-
-
```{r coldata_setup}
# Set up all of the metadata for the samples and experimental design. Use this
From b934b3618607050918f705044d0cf5c1ea36e92a Mon Sep 17 00:00:00 2001
From: daler <dalerr@niddk.nih.gov>
Date: Tue, 25 Jan 2022 11:55:23 -0500
Subject: [PATCH 03/91] try adding actions config
---
.github/workflows/main.yaml | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)
create mode 100644 .github/workflows/main.yaml
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
new file mode 100644
index 00000000..2a27947a
--- /dev/null
+++ b/.github/workflows/main.yaml
@@ -0,0 +1,30 @@
+on: [push]
+jobs:
+
+ build:
+ runs-on: ubuntu-latest
+ container: continuumio/miniconda3
+ steps:
+
+ - uses: actions/checkout@v1
+
+ - name: Cache conda env
+ id: cache-conda
+ uses: actions/cache@v1
+ with:
+ path: /opt/conda
+ key: ${{ hashFiles('env.yml') }}
+
+ - name: Rebuild cache
+ if: steps.cache-conda.outputs.cache-hit != 'true'
+ run: |
+ conda config --add channels defaults
+ conda config --add channels bioconda
+ conda config --add channels conda-forge
+ conda env create -n lcdb-wf-test --file env.yml
+
+ - name: STAR available?
+ shell: bash
+ run: |
+ source activate lcdb-wf-test
+ STAR --version
From b100c363aa752919f5eae91d99637d59c8e5b21b Mon Sep 17 00:00:00 2001
From: daler <dalerr@niddk.nih.gov>
Date: Tue, 25 Jan 2022 11:58:58 -0500
Subject: [PATCH 04/91] create backup circleci config
---
.circleci/{config.yml => config.bak} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
rename .circleci/{config.yml => config.bak} (100%)
diff --git a/.circleci/config.yml b/.circleci/config.bak
similarity index 100%
rename from .circleci/config.yml
rename to .circleci/config.bak
From b8eeee21f0d5609d0570c795f20113236f9daa42 Mon Sep 17 00:00:00 2001
From: daler <dalerr@niddk.nih.gov>
Date: Tue, 25 Jan 2022 12:08:07 -0500
Subject: [PATCH 05/91] mv circleci dir
---
{.circleci => .circleci.back}/config.bak | 0
1 file changed, 0 insertions(+), 0 deletions(-)
rename {.circleci => .circleci.back}/config.bak (100%)
diff --git a/.circleci/config.bak b/.circleci.back/config.bak
similarity index 100%
rename from .circleci/config.bak
rename to .circleci.back/config.bak
From 49160a15ddd68e5a2b6d9fcdcc18609dab5a7274 Mon Sep 17 00:00:00 2001
From: daler <dalerr@niddk.nih.gov>
Date: Tue, 25 Jan 2022 12:30:11 -0500
Subject: [PATCH 06/91] use mamba, and build r env too
---
.github/workflows/main.yaml | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
index 2a27947a..062fec00 100644
--- a/.github/workflows/main.yaml
+++ b/.github/workflows/main.yaml
@@ -21,7 +21,9 @@ jobs:
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
- conda env create -n lcdb-wf-test --file env.yml
+ conda install mamba -y
+ mamba env create -n lcdb-wf-test --file env.yml
+ mamba env create -n lcdb-wf-test-r --file env-r.yml
- name: STAR available?
shell: bash
From 2a6b3d426b4f2b5784f0da05bafbc0be6e9b33b4 Mon Sep 17 00:00:00 2001
From: daler <dalerr@niddk.nih.gov>
Date: Sun, 18 Sep 2022 21:38:24 -0400
Subject: [PATCH 07/91] remove builds from env-r.yml
---
env-r.yml | 795 +++++++++++++++++++++++++++---------------------------
1 file changed, 396 insertions(+), 399 deletions(-)
diff --git a/env-r.yml b/env-r.yml
index d4076b0f..3d4f02c7 100644
--- a/env-r.yml
+++ b/env-r.yml
@@ -1,403 +1,400 @@
-name: null
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- - _libgcc_mutex=0.1=conda_forge
- - _openmp_mutex=4.5=1_gnu
- - _r-mutex=1.0.1=anacondar_1
- - binutils_impl_linux-64=2.36.1=h193b22a_2
- - binutils_linux-64=2.36=hf3e587d_1
- - bioconductor-all=1.36.0=r41hdfd78af_0
- - bioconductor-annotate=1.72.0=r41hdfd78af_0
- - bioconductor-annotationdbi=1.56.1=r41hdfd78af_0
- - bioconductor-annotationfilter=1.18.0=r41hdfd78af_0
- - bioconductor-annotationhub=3.2.0=r41hdfd78af_0
- - bioconductor-apeglm=1.16.0=r41h399db7b_0
- - bioconductor-biobase=2.54.0=r41hd029910_0
- - bioconductor-biocfilecache=2.2.0=r41hdfd78af_0
- - bioconductor-biocgenerics=0.40.0=r41hdfd78af_0
- - bioconductor-biocio=1.4.0=r41hdfd78af_0
- - bioconductor-biocparallel=1.28.0=r41h399db7b_0
- - bioconductor-biocversion=3.14.0=r41hdfd78af_0
- - bioconductor-biomart=2.50.0=r41hdfd78af_0
- - bioconductor-biostrings=2.62.0=r41hd029910_0
- - bioconductor-clusterprofiler=4.2.0=r41hdfd78af_0
- - bioconductor-complexheatmap=2.10.0=r41hdfd78af_0
- - bioconductor-consensusclusterplus=1.58.0=r41hdfd78af_0
- - bioconductor-degreport=1.30.0=r41hdfd78af_0
- - bioconductor-delayedarray=0.20.0=r41hd029910_0
- - bioconductor-deseq2=1.34.0=r41h399db7b_0
- - bioconductor-do.db=2.9=r41hdfd78af_12
- - bioconductor-dose=3.20.0=r41hdfd78af_0
- - bioconductor-dupradar=1.24.0=r41hdfd78af_0
- - bioconductor-edger=3.36.0=r41h399db7b_0
- - bioconductor-enrichplot=1.14.1=r41hdfd78af_0
- - bioconductor-ensembldb=2.18.1=r41hdfd78af_0
- - bioconductor-fgsea=1.20.0=r41h399db7b_0
- - bioconductor-genefilter=1.76.0=r41hba52eb8_0
- - bioconductor-geneplotter=1.72.0=r41hdfd78af_0
- - bioconductor-genomeinfodb=1.30.0=r41hdfd78af_0
- - bioconductor-genomeinfodbdata=1.2.7=r41hdfd78af_1
- - bioconductor-genomicalignments=1.30.0=r41hd029910_0
- - bioconductor-genomicfeatures=1.46.1=r41hdfd78af_0
- - bioconductor-genomicranges=1.46.0=r41hd029910_0
- - bioconductor-ggtree=3.2.0=r41hdfd78af_0
- - bioconductor-go.db=3.14.0=r41hdfd78af_0
- - bioconductor-gosemsim=2.20.0=r41h399db7b_0
- - bioconductor-graph=1.72.0=r41hd029910_0
- - bioconductor-graphite=1.40.0=r41hdfd78af_0
- - bioconductor-ihw=1.22.0=r41hdfd78af_0
- - bioconductor-interactivedisplaybase=1.32.0=r41hdfd78af_0
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- - bioconductor-limma=3.50.0=r41hd029910_0
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- - bioconductor-matrixgenerics=1.6.0=r41hdfd78af_0
- - bioconductor-protgenerics=1.26.0=r41hdfd78af_0
- - bioconductor-qvalue=2.26.0=r41hdfd78af_0
- - bioconductor-reactome.db=1.77.0=r41hdfd78af_0
- - bioconductor-reactomepa=1.38.0=r41hdfd78af_0
- - bioconductor-rhdf5=2.38.0=r41hfe70e90_1
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- - bioconductor-sva=3.42.0=r41hd029910_0
- - bioconductor-treeio=1.18.0=r41hdfd78af_0
- - bioconductor-tximport=1.22.0=r41hdfd78af_0
- - bioconductor-xvector=0.34.0=r41hd029910_0
- - bioconductor-zlibbioc=1.40.0=r41hd029910_0
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- - ca-certificates=2021.10.8=ha878542_0
- - cairo=1.16.0=h6cf1ce9_1008
- - curl=7.80.0=h2574ce0_0
- - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
- - font-ttf-inconsolata=3.000=h77eed37_0
- - font-ttf-source-code-pro=2.038=h77eed37_0
- - font-ttf-ubuntu=0.83=hab24e00_0
- - fontconfig=2.13.1=hba837de_1005
- - fonts-conda-ecosystem=1=0
- - fonts-conda-forge=1=0
- - freetype=2.10.4=h0708190_1
- - fribidi=1.0.10=h36c2ea0_0
- - gcc_impl_linux-64=9.4.0=h03d3576_11
- - gcc_linux-64=9.4.0=h391b98a_1
- - gettext=0.19.8.1=h73d1719_1008
- - gfortran_impl_linux-64=9.4.0=h0003116_11
- - gfortran_linux-64=9.4.0=hf0ab688_1
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- - gxx_impl_linux-64=9.4.0=h03d3576_11
- - gxx_linux-64=9.4.0=h0316aca_1
- - harfbuzz=3.1.1=h83ec7ef_0
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- - jpeg=9d=h36c2ea0_0
- - kernel-headers_linux-64=2.6.32=he073ed8_15
- - krb5=1.19.2=hcc1bbae_3
- - ld_impl_linux-64=2.36.1=hea4e1c9_2
- - lerc=3.0=h9c3ff4c_0
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- - libcurl=7.80.0=h2574ce0_0
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+ - r-qap=0.1_1
+ - r-r6=2.5.1
+ - r-rappdirs=0.3.3
+ - r-rcmdcheck=1.4.0
+ - r-rcolorbrewer=1.1_2
+ - r-rcpp=1.0.7
+ - r-rcpparmadillo=0.10.7.3.0
+ - r-rcppeigen=0.3.3.9.1
+ - r-rcppnumerical=0.4_0
+ - r-rcurl=1.98_1.5
+ - r-readr=2.1.0
+ - r-registry=0.5_1
+ - r-rematch2=2.1.2
+ - r-remotes=2.4.1
+ - r-reshape=0.8.8
+ - r-reshape2=1.4.4
+ - r-restfulr=0.0.13
+ - r-rex=1.2.0
+ - r-rjson=0.2.20
+ - r-rlang=0.4.12
+ - r-rmarkdown=2.11
+ - r-roxygen2=7.1.2
+ - r-rprojroot=2.0.2
+ - r-rsqlite=2.2.8
+ - r-rstudioapi=0.13
+ - r-rvcheck=0.1.8
+ - r-rversions=2.1.1
+ - r-sass=0.4.0
+ - r-scales=1.1.1
+ - r-scatterpie=0.1.6
+ - r-seriation=1.3.1
+ - r-sessioninfo=1.2.1
+ - r-shadowtext=0.0.9
+ - r-shape=1.4.6
+ - r-shiny=1.7.1
+ - r-slam=0.1_48
+ - r-snow=0.4_4
+ - r-sourcetools=0.1.7
+ - r-sparsem=1.81
+ - r-spp=1.16.0
+ - r-squarem=2021.1
+ - r-stringi=1.7.5
+ - r-stringr=1.4.0
+ - r-survival=3.2_13
+ - r-sys=3.4
+ - r-testthat=3.1.0
+ - r-tibble=3.1.6
+ - r-tidygraph=1.2.0
+ - r-tidyr=1.1.4
+ - r-tidyselect=1.1.1
+ - r-tidytree=0.3.6
+ - r-tinytex=0.35
+ - r-tmvnsim=1.0_2
+ - r-truncnorm=1.0_8
+ - r-tsp=1.1_11
+ - r-tweenr=1.0.2
+ - r-tzdb=0.2.0
+ - r-upsetr=1.4.0
+ - r-usethis=2.1.3
+ - r-utf8=1.2.2
+ - r-vctrs=0.3.8
+ - r-viridis=0.6.2
+ - r-viridislite=0.4.0
+ - r-vroom=1.5.6
+ - r-waldo=0.3.1
+ - r-webshot=0.5.2
+ - r-whisker=0.4
+ - r-withr=2.4.2
+ - r-xfun=0.28
+ - r-xml=3.99_0.8
+ - r-xml2=1.3.2
+ - r-xopen=1.0.0
+ - r-xtable=1.8_4
+ - r-yaml=2.2.1
+ - r-yulab.utils=0.0.4
+ - r-zip=2.2.0
+ - readline=8.1
+ - sed=4.8
+ - sysroot_linux-64=2.12
+ - tk=8.6.11
+ - tktable=2.10
+ - xorg-kbproto=1.0.7
+ - xorg-libice=1.0.10
+ - xorg-libsm=1.2.3
+ - xorg-libx11=1.7.2
+ - xorg-libxau=1.0.9
+ - xorg-libxdmcp=1.1.3
+ - xorg-libxext=1.3.4
+ - xorg-libxrender=0.9.10
+ - xorg-libxt=1.2.1
+ - xorg-renderproto=0.11.1
+ - xorg-xextproto=7.3.0
+ - xorg-xproto=7.0.31
+ - xz=5.2.5
+ - zlib=1.2.11
+ - zstd=1.5.0
From 3a30e1cf4ad8c6ec47fae6b16e54c9f5543cbb36 Mon Sep 17 00:00:00 2001
From: daler <dalerr@niddk.nih.gov>
Date: Sun, 18 Sep 2022 21:45:12 -0400
Subject: [PATCH 08/91] update env-r.yml export
---
env-r.yml | 83 +++++++++++++++++++++++++++----------------------------
1 file changed, 40 insertions(+), 43 deletions(-)
diff --git a/env-r.yml b/env-r.yml
index 3d4f02c7..a4fec770 100644
--- a/env-r.yml
+++ b/env-r.yml
@@ -6,7 +6,6 @@ dependencies:
- _openmp_mutex=4.5
- _r-mutex=1.0.1
- binutils_impl_linux-64=2.36.1
- - binutils_linux-64=2.36
- bioconductor-all=1.36.0
- bioconductor-annotate=1.72.0
- bioconductor-annotationdbi=1.56.1
@@ -76,69 +75,67 @@ dependencies:
- c-ares=1.18.1
- ca-certificates=2021.10.8
- cairo=1.16.0
- - curl=7.80.0
+ - curl=7.83.1
+ - expat=2.4.8
- font-ttf-dejavu-sans-mono=2.37
- font-ttf-inconsolata=3.000
- font-ttf-source-code-pro=2.038
- font-ttf-ubuntu=0.83
- - fontconfig=2.13.1
+ - fontconfig=2.14.0
- fonts-conda-ecosystem=1
- fonts-conda-forge=1
- freetype=2.10.4
- fribidi=1.0.10
- - gcc_impl_linux-64=9.4.0
- - gcc_linux-64=9.4.0
+ - gcc_impl_linux-64=12.1.0
- gettext=0.19.8.1
- - gfortran_impl_linux-64=9.4.0
- - gfortran_linux-64=9.4.0
+ - gfortran_impl_linux-64=12.1.0
- gmp=6.2.1
- graphite2=1.3.13
- gsl=2.7
- - gxx_impl_linux-64=9.4.0
- - gxx_linux-64=9.4.0
- - harfbuzz=3.1.1
- - icu=68.2
- - jbig=2.1
- - jpeg=9d
+ - gxx_impl_linux-64=12.1.0
+ - harfbuzz=5.1.0
+ - icu=70.1
+ - jpeg=9e
- kernel-headers_linux-64=2.6.32
- - krb5=1.19.2
+ - keyutils=1.6.1
+ - krb5=1.19.3
- ld_impl_linux-64=2.36.1
- lerc=3.0
- libblas=3.9.0
- libcblas=3.9.0
- - libcurl=7.80.0
- - libdeflate=1.8
+ - libcurl=7.83.1
+ - libdeflate=1.12
- libedit=3.1.20191231
- libev=4.33
- libffi=3.4.2
- - libgcc-devel_linux-64=9.4.0
- - libgcc-ng=11.2.0
- - libgfortran-ng=11.2.0
- - libgfortran5=11.2.0
+ - libgcc-devel_linux-64=12.1.0
+ - libgcc-ng=12.1.0
+ - libgfortran-ng=12.1.0
+ - libgfortran5=12.1.0
- libgit2=1.3.0
- - libglib=2.70.0
- - libgomp=11.2.0
+ - libglib=2.72.1
+ - libgomp=12.1.0
- libiconv=1.16
- liblapack=3.9.0
- - libnghttp2=1.43.0
- - libopenblas=0.3.18
- - libpng=1.6.37
- - libsanitizer=9.4.0
+ - libnghttp2=1.47.0
+ - libopenblas=0.3.21
+ - libpng=1.6.38
+ - libsanitizer=12.1.0
- libssh2=1.10.0
- - libstdcxx-devel_linux-64=9.4.0
- - libstdcxx-ng=11.2.0
- - libtiff=4.3.0
+ - libstdcxx-devel_linux-64=12.1.0
+ - libstdcxx-ng=12.1.0
+ - libtiff=4.4.0
- libuuid=2.32.1
- libwebp-base=1.2.1
- libxcb=1.13
- - libxml2=2.9.12
- - libzlib=1.2.11
+ - libxml2=2.9.14
+ - libzlib=1.2.12
- lz4-c=1.9.3
- make=4.3
- - ncurses=6.2
- - openssl=1.1.1l
+ - ncurses=6.3
+ - openssl=1.1.1q
- pandoc=2.16.1
- - pango=1.48.10
+ - pango=1.50.9
- pcre=8.45
- pcre2=10.37
- pixman=0.40.0
@@ -150,7 +147,7 @@ dependencies:
- r-assertthat=0.2.1
- r-babelgene=21.4
- r-backports=1.3.0
- - r-base=4.1.1
+ - r-base=4.1.3
- r-base64enc=0.1_3
- r-bbmle=1.0.24
- r-bdsmatrix=1.3_4
@@ -237,7 +234,7 @@ dependencies:
- r-gridextra=2.3
- r-gridgraphics=0.5_1
- r-gtable=0.3.0
- - r-gtools=3.9.2
+ - r-gtools=3.9.2.2
- r-heatmaply=1.3.0
- r-hexbin=1.28.2
- r-highr=0.9
@@ -279,7 +276,7 @@ dependencies:
- r-munsell=0.5.0
- r-mvtnorm=1.1_3
- r-nlme=3.1_153
- - r-nozzle.r1=1.1_1
+ - r-nozzle.r1=1.1_1.1
- r-numderiv=2016.8_1.1
- r-openssl=1.4.5
- r-openxlsx=4.2.4
@@ -311,7 +308,7 @@ dependencies:
- r-rcpparmadillo=0.10.7.3.0
- r-rcppeigen=0.3.3.9.1
- r-rcppnumerical=0.4_0
- - r-rcurl=1.98_1.5
+ - r-rcurl=1.98_1.8
- r-readr=2.1.0
- r-registry=0.5_1
- r-rematch2=2.1.2
@@ -343,7 +340,7 @@ dependencies:
- r-sparsem=1.81
- r-spp=1.16.0
- r-squarem=2021.1
- - r-stringi=1.7.5
+ - r-stringi=1.7.8
- r-stringr=1.4.0
- r-survival=3.2_13
- r-sys=3.4
@@ -378,10 +375,10 @@ dependencies:
- r-yaml=2.2.1
- r-yulab.utils=0.0.4
- r-zip=2.2.0
- - readline=8.1
+ - readline=8.1.2
- sed=4.8
- sysroot_linux-64=2.12
- - tk=8.6.11
+ - tk=8.6.12
- tktable=2.10
- xorg-kbproto=1.0.7
- xorg-libice=1.0.10
@@ -396,5 +393,5 @@ dependencies:
- xorg-xextproto=7.3.0
- xorg-xproto=7.0.31
- xz=5.2.5
- - zlib=1.2.11
- - zstd=1.5.0
+ - zlib=1.2.12
+ - zstd=1.5.2
From d9be76267f357130e694e3320e2ff7b94da1cd90 Mon Sep 17 00:00:00 2001
From: daler <dalerr@niddk.nih.gov>
Date: Sun, 18 Sep 2022 21:46:01 -0400
Subject: [PATCH 09/91] remove builds from env.yml
---
env.yml | 684 ++++++++++++++++++++++++++++----------------------------
1 file changed, 342 insertions(+), 342 deletions(-)
diff --git a/env.yml b/env.yml
index fb7f9eb7..f0b068e2 100644
--- a/env.yml
+++ b/env.yml
@@ -3,345 +3,345 @@ channels:
- bioconda
- defaults
dependencies:
- - _libgcc_mutex=0.1=conda_forge
- - _openmp_mutex=4.5=1_llvm
- - _r-mutex=1.0.1=anacondar_1
- - aiohttp=3.7.4=py39h3811e60_0
- - alsa-lib=1.2.3=h516909a_0
- - amply=0.1.4=py_0
- - apipkg=1.5=py_0
- - appdirs=1.4.4=pyh9f0ad1d_0
- - argcomplete=1.12.3=pyhd8ed1ab_2
- - argh=0.26.2=pyh9f0ad1d_1002
- - async-timeout=3.0.1=py_1000
- - attrs=20.3.0=pyhd3deb0d_0
- - azure-common=1.1.27=pyhd8ed1ab_0
- - azure-core=1.12.0=pyhd8ed1ab_0
- - azure-storage-blob=12.8.1=pyhd8ed1ab_0
- - backcall=0.2.0=pyh9f0ad1d_0
- - backports=1.0=py_2
- - backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
- - bedtools=2.30.0=h7d7f7ad_1
- - binutils_impl_linux-64=2.35.1=h193b22a_2
- - binutils_linux-64=2.35=h67ddf6f_30
- - biopython=1.78=py39h3811e60_2
- - blinker=1.4=py_1
- - boost-cpp=1.74.0=hc6e9bd1_2
- - boto=2.49.0=py_0
- - boto3=1.17.56=pyhd8ed1ab_0
- - botocore=1.20.57=pyhd8ed1ab_0
- - bowtie=1.3.0=py39h176da8b_2
- - bowtie2=2.4.2=py39hc9c6fcd_2
- - brotlipy=0.7.0=py39h3811e60_1001
- - bwidget=1.9.14=0
- - bx-python=0.8.11=py39h5d76eff_1
- - bzip2=1.0.8=h7f98852_4
- - c-ares=1.17.1=h7f98852_1
- - ca-certificates=2021.4.13=h06a4308_1
- - cachetools=4.2.1=pyhd8ed1ab_0
- - cairo=1.16.0=h6cf1ce9_1008
- - certifi=2020.12.5=py39hf3d152e_1
- - cffi=1.14.5=py39he32792d_0
- - chardet=4.0.0=py39hf3d152e_1
- - click=7.1.2=pyh9f0ad1d_0
- - coincbc=2.10.5=hcee13e7_1
- - colorama=0.4.4=pyh9f0ad1d_0
- - coloredlogs=15.0=py39hf3d152e_0
- - colormath=3.0.0=py_2
- - commonmark=0.9.1=py_0
- - configargparse=1.4=pyhd8ed1ab_0
- - cryptography=3.4.7=py39hbca0aa6_0
- - curl=7.76.1=h979ede3_1
- - cutadapt=3.4=py39h38f01e4_1
- - cycler=0.10.0=py_2
- - datrie=0.8.2=py39h07f9747_1
- - dbus=1.13.18=hb2f20db_0
- - decorator=5.0.7=pyhd8ed1ab_0
- - deeptools=3.5.1=py_0
- - deeptoolsintervals=0.1.9=py39h38f01e4_3
- - dnaio=0.5.0=py39h38f01e4_1
- - docutils=0.17.1=py39hf3d152e_0
- - execnet=1.8.0=pyh44b312d_0
- - expat=2.3.0=h9c3ff4c_0
- - fastq-screen=0.14.0=pl5262hdfd78af_1
- - fastqc=0.11.9=hdfd78af_1
- - filelock=3.0.12=pyh9f0ad1d_0
- - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
- - fontconfig=2.13.1=hba837de_1005
- - freetype=2.10.4=h0708190_1
- - fribidi=1.0.10=h516909a_0
- - future=0.18.2=py39hf3d152e_3
- - gat=1.3.6=py39hd1f1204_3
- - gcc_impl_linux-64=9.3.0=h70c0ae5_19
- - gcc_linux-64=9.3.0=hf25ea35_30
- - gettext=0.21.0=hf68c758_0
- - gffread=0.12.1=h2e03b76_1
- - gffutils=0.10.1=pyh864c0ab_1
- - gfortran_impl_linux-64=9.3.0=hc4a2995_19
- - gfortran_linux-64=9.3.0=hdc58fab_30
- - giflib=5.2.1=h516909a_2
- - gitdb=4.0.7=pyhd8ed1ab_0
- - gitpython=3.1.15=pyhd8ed1ab_0
- - glib=2.68.1=h9c3ff4c_0
- - glib-tools=2.68.1=h9c3ff4c_0
- - google-api-core=1.26.2=pyhd8ed1ab_0
- - google-auth=1.29.0=pyhd3eb1b0_0
- - google-cloud-core=1.6.0=pyhd3eb1b0_0
- - google-cloud-storage=1.37.1=pyhd3eb1b0_0
- - google-crc32c=1.1.2=py39hb81f231_0
- - google-resumable-media=1.2.0=pyhd3deb0d_0
- - googleapis-common-protos=1.53.0=py39hf3d152e_0
- - graphite2=1.3.14=h23475e2_0
- - gsl=2.6=he838d99_2
- - gst-plugins-base=1.18.4=hf529b03_1
- - gstreamer=1.18.4=h76c114f_1
- - gxx_impl_linux-64=9.3.0=hd87eabc_19
- - gxx_linux-64=9.3.0=h3fbe746_30
- - harfbuzz=2.8.0=h83ec7ef_1
- - hdf5=1.10.6=nompi_h6a2412b_1114
- - hisat2=2.2.1=h1b792b2_3
- - htslib=1.12=h9093b5e_1
- - humanfriendly=9.1=py39hf3d152e_0
- - icu=68.1=h58526e2_0
- - idna=2.10=pyh9f0ad1d_0
- - importlib-metadata=4.0.1=py39hf3d152e_0
- - importlib_metadata=4.0.1=hd8ed1ab_0
- - iniconfig=1.1.1=pyh9f0ad1d_0
- - intervalstats=1.01=0
- - ipython=7.22.0=py39hef51801_0
- - ipython_genutils=0.2.0=py_1
- - isa-l=2.30.0=ha770c72_4
- - isodate=0.6.0=py_1
- - jedi=0.18.0=py39hf3d152e_2
- - jemalloc=5.2.1=h9c3ff4c_5
- - jinja2=2.11.3=pyh44b312d_0
- - jmespath=0.10.0=pyh9f0ad1d_0
- - jpeg=9d=h516909a_0
- - jsonschema=3.2.0=pyhd8ed1ab_3
- - jupyter_core=4.7.1=py39hf3d152e_0
- - kallisto=0.46.2=h60f4f9f_2
- - kernel-headers_linux-64=2.6.32=h77966d4_13
- - kiwisolver=1.3.1=py39h1a9c180_1
- - krb5=1.17.2=h926e7f8_0
- - lcms2=2.12=hddcbb42_0
- - ld_impl_linux-64=2.35.1=hea4e1c9_2
- - libblas=3.9.0=8_mkl
- - libcblas=3.9.0=8_mkl
- - libclang=11.1.0=default_ha53f305_0
- - libcrc32c=1.1.1=he1b5a44_2
- - libcurl=7.76.1=hc4aaa36_1
- - libdeflate=1.7=h7f98852_5
- - libedit=3.1.20210216=h27cfd23_1
- - libev=4.33=h516909a_1
- - libevent=2.1.10=hcdb4288_3
- - libffi=3.3=h58526e2_2
- - libgcc-devel_linux-64=9.3.0=h7864c58_19
- - libgcc-ng=9.3.0=h2828fa1_19
- - libgd=2.3.2=h78a0170_0
- - libgfortran-ng=9.3.0=hff62375_19
- - libgfortran5=9.3.0=hff62375_19
- - libglib=2.68.1=h3e27bee_0
- - libgomp=9.3.0=h2828fa1_19
- - libiconv=1.16=h516909a_0
- - liblapack=3.9.0=8_mkl
- - libllvm11=11.1.0=hf817b99_2
- - libnghttp2=1.43.0=h812cca2_0
- - libopenblas=0.3.13=pthreads_h8fe5266_0
- - libpng=1.6.37=hed695b0_2
- - libpq=13.2=hfd2b0eb_2
- - libprotobuf=3.15.8=h780b84a_0
- - libssh2=1.9.0=ha56f1ee_6
- - libstdcxx-devel_linux-64=9.3.0=hb016644_19
- - libstdcxx-ng=9.3.0=h6de172a_19
- - libtiff=4.2.0=hdc55705_1
- - libuuid=2.32.1=h14c3975_1000
- - libwebp=1.2.0=h3452ae3_0
- - libwebp-base=1.2.0=h7f98852_2
- - libxcb=1.14=h7b6447c_0
- - libxkbcommon=1.0.3=he3ba5ed_0
- - libxml2=2.9.10=h72842e0_4
- - llvm-openmp=11.1.0=h4bd325d_1
- - lz4-c=1.9.3=h9c3ff4c_0
- - lzo=2.10=h516909a_1000
- - lzstring=1.0.4=py_1001
- - make=4.3=hd18ef5c_1
- - markdown=3.3.4=pyhd8ed1ab_0
- - markupsafe=1.1.1=py39h3811e60_3
- - matplotlib=3.4.1=py39hf3d152e_0
- - matplotlib-base=3.4.1=py39h2fa2bec_0
- - mkl=2020.4=h726a3e6_304
- - more-itertools=8.7.0=pyhd8ed1ab_0
- - msrest=0.6.21=pyh44b312d_0
- - multidict=5.1.0=py39h3811e60_1
- - multiqc=1.10.1=py_0
- - mysql-common=8.0.23=ha770c72_1
- - mysql-connector-c=6.1.11=h6eb9d5d_1007
- - mysql-libs=8.0.23=h935591d_1
- - nbformat=5.1.3=pyhd8ed1ab_0
- - ncbi-ngs-sdk=2.11.0=hff44eed_0
- - ncurses=6.2=h58526e2_4
- - networkx=2.5=py_0
- - nspr=4.30=h9c3ff4c_0
- - nss=3.64=hb5efdd6_0
- - numpy=1.20.2=py39hdbf815f_0
- - oauthlib=3.1.0=py_0
- - olefile=0.46=pyh9f0ad1d_1
- - openblas=0.3.13=pthreads_h4748800_0
- - openjdk=11.0.9.1=h5cc2fde_1
- - openssl=1.1.1k=h7f98852_0
- - packaging=20.9=pyh44b312d_0
- - pandas=1.2.4=py39hde0f152_0
- - pandoc=2.12=h7f98852_0
- - pango=1.48.4=hb8ff022_0
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- - patsy=0.5.1=py_0
- - pcre=8.44=he1b5a44_0
- - pcre2=10.36=h032f7d1_1
- - perl=5.26.2=h36c2ea0_1008
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- - perl-exporter=5.72=pl526_1
- - perl-extutils-makemaker=7.36=pl526_1
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- - perl-gd=2.68=pl526he941832_0
- - perl-gdgraph=1.54=pl526_0
- - perl-gdtextutil=0.86=pl526h14c3975_5
- - perl-mime-base64=3.15=pl526_1
- - perl-parent=0.236=pl526_1
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- - pexpect=4.8.0=pyh9f0ad1d_2
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- - pigz=2.6=h27826a3_0
- - pillow=8.2.0=py39he98fc37_0
- - pip=21.0.1=pyhd8ed1ab_0
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- - plotly=4.14.3=pyh44b312d_0
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- - prompt-toolkit=3.0.18=pyha770c72_0
- - protobuf=3.15.8=py39he80948d_0
- - psutil=5.8.0=py39h3811e60_1
- - ptyprocess=0.7.0=pyhd3deb0d_0
- - pulp=2.4=py39hf3d152e_0
- - py=1.10.0=pyhd3deb0d_0
- - py2bit=0.3.0=py39h38f01e4_5
- - pyasn1=0.4.8=py_0
- - pyasn1-modules=0.2.8=py_0
- - pybedtools=0.8.2=py39h39abbe0_1
- - pybigwig=0.3.18=py39h015b436_1
- - pycparser=2.20=pyh9f0ad1d_2
- - pyfaidx=0.5.9.5=pyh3252c3a_0
- - pygments=2.8.1=pyhd8ed1ab_0
- - pyjwt=2.0.1=pyhd8ed1ab_1
- - pyopenssl=20.0.1=pyhd8ed1ab_0
- - pyparsing=2.4.7=pyh9f0ad1d_0
- - pyqt=5.12.3=py39hf3d152e_7
- - pyqt-impl=5.12.3=py39h0fcd23e_7
- - pyqt5-sip=4.19.18=py39he80948d_7
- - pyqtchart=5.12=py39h0fcd23e_7
- - pyqtwebengine=5.12.1=py39h0fcd23e_7
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- - pysam=0.16.0.1=py39h051187c_3
- - pysocks=1.7.1=py39hf3d152e_3
- - pytest=6.2.3=py39hf3d152e_0
- - pytest-forked=1.3.0=pyhd3deb0d_0
- - pytest-xdist=2.2.1=pyhd8ed1ab_0
- - python=3.9.4=hdb3f193_0
- - python-dateutil=2.8.1=py_0
- - python-isal=0.10.0=py39h3811e60_0
- - python-lzo=1.12=py39h265373d_1003
- - python_abi=3.9=1_cp39
- - pytz=2021.1=pyhd8ed1ab_0
- - pyyaml=5.4.1=py39h3811e60_0
- - qt=5.12.9=hda022c4_4
- - r-base=4.0.3=h349a78a_8
- - ratelimiter=1.2.0=py_1002
- - readline=8.1=h46c0cb4_0
- - requests=2.25.1=pyhd3deb0d_0
- - requests-oauthlib=1.3.0=pyh9f0ad1d_0
- - retrying=1.3.3=py_2
- - rich=10.1.0=py39hf3d152e_0
- - rsa=4.7.2=pyh44b312d_0
- - rseqc=4.0.0=py39h38f01e4_1
- - s3transfer=0.4.2=pyhd8ed1ab_0
- - salmon=1.4.0=h84f40af_1
- - samtools=1.12=h9aed4be_1
- - scipy=1.6.2=py39hee8e79c_0
- - seaborn=0.11.1=ha770c72_0
- - seaborn-base=0.11.1=pyhd8ed1ab_1
- - sed=4.8=he412f7d_0
- - setuptools=52.0.0=py39h06a4308_0
- - simplejson=3.17.2=py39h3811e60_2
- - six=1.15.0=pyh9f0ad1d_0
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- - smmap=3.0.5=pyh44b312d_0
- - snakemake-minimal=6.2.1=pyhdfd78af_0
- - spectra=0.0.11=py_1
- - sqlite=3.35.5=h74cdb3f_0
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- - star=2.7.8a=h9ee0642_1
- - statsmodels=0.12.2=py39hce5d2b2_0
- - stopit=1.1.2=py_0
- - subread=2.0.1=h5bf99c6_1
- - sysroot_linux-64=2.12=h77966d4_13
- - tbb=2020.3=hfd86e86_0
- - tk=8.6.10=hed695b0_1
- - tktable=2.10=hb7b940f_3
- - toml=0.10.2=pyhd8ed1ab_0
- - toposort=1.6=pyhd8ed1ab_0
- - tornado=6.1=py39h3811e60_1
- - trackhub=0.2.4=pyh864c0ab_2
- - traitlets=5.0.5=py_0
- - typing-extensions=3.7.4.3=0
- - typing_extensions=3.7.4.3=py_0
- - tzdata=2021a=he74cb21_0
- - ucsc-bedgraphtobigwig=377=h0b8a92a_2
- - ucsc-bedsort=377=h0b8a92a_3
- - ucsc-bedtobigbed=377=h0b8a92a_2
- - ucsc-bigwigmerge=377=h0b8a92a_2
- - ucsc-fetchchromsizes=377=h0b8a92a_2
- - ucsc-genepredtobed=377=h0b8a92a_4
- - ucsc-gtftogenepred=377=h0b8a92a_4
- - ucsc-liftover=377=h0b8a92a_3
- - ucsc-oligomatch=377=h0b8a92a_2
- - ucsc-twobittofa=377=h0b8a92a_3
- - ucsc-wigtobigwig=377=h0b8a92a_2
- - urllib3=1.26.4=pyhd8ed1ab_0
- - wcwidth=0.2.5=pyh9f0ad1d_2
- - wheel=0.36.2=pyhd3deb0d_0
- - wrapt=1.12.1=py39h3811e60_3
- - xopen=1.1.0=py39hf3d152e_2
- - xorg-fixesproto=5.0=h14c3975_1002
- - xorg-inputproto=2.3.2=h14c3975_1002
- - xorg-kbproto=1.0.7=h14c3975_1002
- - xorg-libice=1.0.10=h516909a_0
- - xorg-libsm=1.2.3=hd9c2040_1000
- - xorg-libx11=1.6.12=h516909a_0
- - xorg-libxext=1.3.4=h516909a_0
- - xorg-libxfixes=5.0.3=h516909a_1004
- - xorg-libxi=1.7.10=h516909a_0
- - xorg-libxrender=0.9.10=h516909a_1002
- - xorg-libxt=1.2.1=h7f98852_0
- - xorg-libxtst=1.2.3=h516909a_1002
- - xorg-recordproto=1.14.2=h516909a_1002
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- - xorg-xproto=7.0.31=h14c3975_1007
- - xz=5.2.5=h516909a_1
- - yaml=0.2.5=h516909a_0
- - yarl=1.5.1=py39h07f9747_0
- - zipp=3.4.1=pyhd8ed1ab_0
- - zlib=1.2.11=h516909a_1010
- - zstd=1.4.9=ha95c52a_0
+ - _libgcc_mutex=0.1
+ - _openmp_mutex=4.5
+ - _r-mutex=1.0.1
+ - aiohttp=3.7.4
+ - alsa-lib=1.2.3
+ - amply=0.1.4
+ - apipkg=1.5
+ - appdirs=1.4.4
+ - argcomplete=1.12.3
+ - argh=0.26.2
+ - async-timeout=3.0.1
+ - attrs=20.3.0
+ - azure-common=1.1.27
+ - azure-core=1.12.0
+ - azure-storage-blob=12.8.1
+ - backcall=0.2.0
+ - backports=1.0
+ - backports.functools_lru_cache=1.6.4
+ - bedtools=2.30.0
+ - binutils_impl_linux-64=2.35.1
+ - binutils_linux-64=2.35
+ - biopython=1.78
+ - blinker=1.4
+ - boost-cpp=1.74.0
+ - boto=2.49.0
+ - boto3=1.17.56
+ - botocore=1.20.57
+ - bowtie=1.3.0
+ - bowtie2=2.4.2
+ - brotlipy=0.7.0
+ - bwidget=1.9.14
+ - bx-python=0.8.11
+ - bzip2=1.0.8
+ - c-ares=1.17.1
+ - ca-certificates=2021.4.13
+ - cachetools=4.2.1
+ - cairo=1.16.0
+ - certifi=2020.12.5
+ - cffi=1.14.5
+ - chardet=4.0.0
+ - click=7.1.2
+ - coincbc=2.10.5
+ - colorama=0.4.4
+ - coloredlogs=15.0
+ - colormath=3.0.0
+ - commonmark=0.9.1
+ - configargparse=1.4
+ - cryptography=3.4.7
+ - curl=7.76.1
+ - cutadapt=3.4
+ - cycler=0.10.0
+ - datrie=0.8.2
+ - dbus=1.13.18
+ - decorator=5.0.7
+ - deeptools=3.5.1
+ - deeptoolsintervals=0.1.9
+ - dnaio=0.5.0
+ - docutils=0.17.1
+ - execnet=1.8.0
+ - expat=2.3.0
+ - fastq-screen=0.14.0
+ - fastqc=0.11.9
+ - filelock=3.0.12
+ - font-ttf-dejavu-sans-mono=2.37
+ - fontconfig=2.13.1
+ - freetype=2.10.4
+ - fribidi=1.0.10
+ - future=0.18.2
+ - gat=1.3.6
+ - gcc_impl_linux-64=9.3.0
+ - gcc_linux-64=9.3.0
+ - gettext=0.21.0
+ - gffread=0.12.1
+ - gffutils=0.10.1
+ - gfortran_impl_linux-64=9.3.0
+ - gfortran_linux-64=9.3.0
+ - giflib=5.2.1
+ - gitdb=4.0.7
+ - gitpython=3.1.15
+ - glib=2.68.1
+ - glib-tools=2.68.1
+ - google-api-core=1.26.2
+ - google-auth=1.29.0
+ - google-cloud-core=1.6.0
+ - google-cloud-storage=1.37.1
+ - google-crc32c=1.1.2
+ - google-resumable-media=1.2.0
+ - googleapis-common-protos=1.53.0
+ - graphite2=1.3.14
+ - gsl=2.6
+ - gst-plugins-base=1.18.4
+ - gstreamer=1.18.4
+ - gxx_impl_linux-64=9.3.0
+ - gxx_linux-64=9.3.0
+ - harfbuzz=2.8.0
+ - hdf5=1.10.6
+ - hisat2=2.2.1
+ - htslib=1.12
+ - humanfriendly=9.1
+ - icu=68.1
+ - idna=2.10
+ - importlib-metadata=4.0.1
+ - importlib_metadata=4.0.1
+ - iniconfig=1.1.1
+ - intervalstats=1.01
+ - ipython=7.22.0
+ - ipython_genutils=0.2.0
+ - isa-l=2.30.0
+ - isodate=0.6.0
+ - jedi=0.18.0
+ - jemalloc=5.2.1
+ - jinja2=2.11.3
+ - jmespath=0.10.0
+ - jpeg=9d
+ - jsonschema=3.2.0
+ - jupyter_core=4.7.1
+ - kallisto=0.46.2
+ - kernel-headers_linux-64=2.6.32
+ - kiwisolver=1.3.1
+ - krb5=1.17.2
+ - lcms2=2.12
+ - ld_impl_linux-64=2.35.1
+ - libblas=3.9.0
+ - libcblas=3.9.0
+ - libclang=11.1.0
+ - libcrc32c=1.1.1
+ - libcurl=7.76.1
+ - libdeflate=1.7
+ - libedit=3.1.20210216
+ - libev=4.33
+ - libevent=2.1.10
+ - libffi=3.3
+ - libgcc-devel_linux-64=9.3.0
+ - libgcc-ng=9.3.0
+ - libgd=2.3.2
+ - libgfortran-ng=9.3.0
+ - libgfortran5=9.3.0
+ - libglib=2.68.1
+ - libgomp=9.3.0
+ - libiconv=1.16
+ - liblapack=3.9.0
+ - libllvm11=11.1.0
+ - libnghttp2=1.43.0
+ - libopenblas=0.3.13
+ - libpng=1.6.37
+ - libpq=13.2
+ - libprotobuf=3.15.8
+ - libssh2=1.9.0
+ - libstdcxx-devel_linux-64=9.3.0
+ - libstdcxx-ng=9.3.0
+ - libtiff=4.2.0
+ - libuuid=2.32.1
+ - libwebp=1.2.0
+ - libwebp-base=1.2.0
+ - libxcb=1.14
+ - libxkbcommon=1.0.3
+ - libxml2=2.9.10
+ - llvm-openmp=11.1.0
+ - lz4-c=1.9.3
+ - lzo=2.10
+ - lzstring=1.0.4
+ - make=4.3
+ - markdown=3.3.4
+ - markupsafe=1.1.1
+ - matplotlib=3.4.1
+ - matplotlib-base=3.4.1
+ - mkl=2020.4
+ - more-itertools=8.7.0
+ - msrest=0.6.21
+ - multidict=5.1.0
+ - multiqc=1.10.1
+ - mysql-common=8.0.23
+ - mysql-connector-c=6.1.11
+ - mysql-libs=8.0.23
+ - nbformat=5.1.3
+ - ncbi-ngs-sdk=2.11.0
+ - ncurses=6.2
+ - networkx=2.5
+ - nspr=4.30
+ - nss=3.64
+ - numpy=1.20.2
+ - oauthlib=3.1.0
+ - olefile=0.46
+ - openblas=0.3.13
+ - openjdk=11.0.9.1
+ - openssl=1.1.1k
+ - packaging=20.9
+ - pandas=1.2.4
+ - pandoc=2.12
+ - pango=1.48.4
+ - parso=0.8.2
+ - patsy=0.5.1
+ - pcre=8.44
+ - pcre2=10.36
+ - perl=5.26.2
+ - perl-app-cpanminus=1.7044
+ - perl-business-isbn=3.004
+ - perl-business-isbn-data=20140910.003
+ - perl-carp=1.38
+ - perl-constant=1.33
+ - perl-data-dumper=2.173
+ - perl-encode=2.88
+ - perl-exporter=5.72
+ - perl-extutils-makemaker=7.36
+ - perl-file-path=2.16
+ - perl-file-temp=0.2304
+ - perl-gd=2.68
+ - perl-gdgraph=1.54
+ - perl-gdtextutil=0.86
+ - perl-mime-base64=3.15
+ - perl-parent=0.236
+ - perl-uri=1.76
+ - perl-xml-libxml=2.0132
+ - perl-xml-namespacesupport=1.12
+ - perl-xml-sax=1.02
+ - perl-xml-sax-base=1.09
+ - perl-xsloader=0.24
+ - pexpect=4.8.0
+ - picard=2.25.2
+ - pickleshare=0.7.5
+ - pigz=2.6
+ - pillow=8.2.0
+ - pip=21.0.1
+ - pixman=0.40.0
+ - plotly=4.14.3
+ - pluggy=0.13.1
+ - preseq=3.1.2
+ - prompt-toolkit=3.0.18
+ - protobuf=3.15.8
+ - psutil=5.8.0
+ - ptyprocess=0.7.0
+ - pulp=2.4
+ - py=1.10.0
+ - py2bit=0.3.0
+ - pyasn1=0.4.8
+ - pyasn1-modules=0.2.8
+ - pybedtools=0.8.2
+ - pybigwig=0.3.18
+ - pycparser=2.20
+ - pyfaidx=0.5.9.5
+ - pygments=2.8.1
+ - pyjwt=2.0.1
+ - pyopenssl=20.0.1
+ - pyparsing=2.4.7
+ - pyqt=5.12.3
+ - pyqt-impl=5.12.3
+ - pyqt5-sip=4.19.18
+ - pyqtchart=5.12
+ - pyqtwebengine=5.12.1
+ - pyrsistent=0.17.3
+ - pysam=0.16.0.1
+ - pysocks=1.7.1
+ - pytest=6.2.3
+ - pytest-forked=1.3.0
+ - pytest-xdist=2.2.1
+ - python=3.9.4
+ - python-dateutil=2.8.1
+ - python-isal=0.10.0
+ - python-lzo=1.12
+ - python_abi=3.9
+ - pytz=2021.1
+ - pyyaml=5.4.1
+ - qt=5.12.9
+ - r-base=4.0.3
+ - ratelimiter=1.2.0
+ - readline=8.1
+ - requests=2.25.1
+ - requests-oauthlib=1.3.0
+ - retrying=1.3.3
+ - rich=10.1.0
+ - rsa=4.7.2
+ - rseqc=4.0.0
+ - s3transfer=0.4.2
+ - salmon=1.4.0
+ - samtools=1.12
+ - scipy=1.6.2
+ - seaborn=0.11.1
+ - seaborn-base=0.11.1
+ - sed=4.8
+ - setuptools=52.0.0
+ - simplejson=3.17.2
+ - six=1.15.0
+ - smart_open=5.0.0
+ - smmap=3.0.5
+ - snakemake-minimal=6.2.1
+ - spectra=0.0.11
+ - sqlite=3.35.5
+ - sra-tools=2.10.0
+ - star=2.7.8a
+ - statsmodels=0.12.2
+ - stopit=1.1.2
+ - subread=2.0.1
+ - sysroot_linux-64=2.12
+ - tbb=2020.3
+ - tk=8.6.10
+ - tktable=2.10
+ - toml=0.10.2
+ - toposort=1.6
+ - tornado=6.1
+ - trackhub=0.2.4
+ - traitlets=5.0.5
+ - typing-extensions=3.7.4.3
+ - typing_extensions=3.7.4.3
+ - tzdata=2021a
+ - ucsc-bedgraphtobigwig=377
+ - ucsc-bedsort=377
+ - ucsc-bedtobigbed=377
+ - ucsc-bigwigmerge=377
+ - ucsc-fetchchromsizes=377
+ - ucsc-genepredtobed=377
+ - ucsc-gtftogenepred=377
+ - ucsc-liftover=377
+ - ucsc-oligomatch=377
+ - ucsc-twobittofa=377
+ - ucsc-wigtobigwig=377
+ - urllib3=1.26.4
+ - wcwidth=0.2.5
+ - wheel=0.36.2
+ - wrapt=1.12.1
+ - xopen=1.1.0
+ - xorg-fixesproto=5.0
+ - xorg-inputproto=2.3.2
+ - xorg-kbproto=1.0.7
+ - xorg-libice=1.0.10
+ - xorg-libsm=1.2.3
+ - xorg-libx11=1.6.12
+ - xorg-libxext=1.3.4
+ - xorg-libxfixes=5.0.3
+ - xorg-libxi=1.7.10
+ - xorg-libxrender=0.9.10
+ - xorg-libxt=1.2.1
+ - xorg-libxtst=1.2.3
+ - xorg-recordproto=1.14.2
+ - xorg-renderproto=0.11.1
+ - xorg-xextproto=7.3.0
+ - xorg-xproto=7.0.31
+ - xz=5.2.5
+ - yaml=0.2.5
+ - yarl=1.5.1
+ - zipp=3.4.1
+ - zlib=1.2.11
+ - zstd=1.4.9
From a1afb65d51d2a79f8b3997f83d083e8415d893df Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov`>
Date: Wed, 9 Nov 2022 15:08:36 -0500
Subject: [PATCH 10/91] fully remove phix
---
include/reference_configs/PhiX.yaml | 11 -----------
test/test_configs/test_chipseq_no_peaks.yaml | 1 -
test/test_configs/test_chipseq_regression.yaml | 1 -
test/test_configs/test_rnaseq_config.yaml | 1 -
4 files changed, 14 deletions(-)
delete mode 100644 include/reference_configs/PhiX.yaml
diff --git a/include/reference_configs/PhiX.yaml b/include/reference_configs/PhiX.yaml
deleted file mode 100644
index 6c2dce35..00000000
--- a/include/reference_configs/PhiX.yaml
+++ /dev/null
@@ -1,11 +0,0 @@
-references:
- phix:
- default:
- genome:
- url: 'ftp://ftp.ncbi.nlm.nih.gov/genomes/Viruses/enterobacteria_phage_phix174_sensu_lato_uid14015/NC_001422.fna'
- postprocess:
- - 'lib.common.gzipped'
- indexes:
- - 'bowtie2'
- - 'hisat2'
- - 'star'
diff --git a/test/test_configs/test_chipseq_no_peaks.yaml b/test/test_configs/test_chipseq_no_peaks.yaml
index f40361c6..ccb0d77f 100644
--- a/test/test_configs/test_chipseq_no_peaks.yaml
+++ b/test/test_configs/test_chipseq_no_peaks.yaml
@@ -27,5 +27,4 @@ merged_bigwigs: {}
include_references:
- '../../include/reference_configs/test.yaml'
- - '../../include/reference_configs/PhiX.yaml'
- '../../include/reference_configs/Drosophila_melanogaster.yaml'
diff --git a/test/test_configs/test_chipseq_regression.yaml b/test/test_configs/test_chipseq_regression.yaml
index 6b91f5db..220dfaed 100644
--- a/test/test_configs/test_chipseq_regression.yaml
+++ b/test/test_configs/test_chipseq_regression.yaml
@@ -36,5 +36,4 @@ merged_bigwigs: {}
include_references:
- '../../include/reference_configs/test.yaml'
- - '../../include/reference_configs/PhiX.yaml'
- '../../include/reference_configs/Drosophila_melanogaster.yaml'
diff --git a/test/test_configs/test_rnaseq_config.yaml b/test/test_configs/test_rnaseq_config.yaml
index ad4a06c7..93ab5e0c 100644
--- a/test/test_configs/test_rnaseq_config.yaml
+++ b/test/test_configs/test_rnaseq_config.yaml
@@ -43,5 +43,4 @@ fastq_screen:
include_references:
- '../../include/reference_configs/test.yaml'
- - '../../include/reference_configs/PhiX.yaml'
- '../../include/reference_configs/Drosophila_melanogaster.yaml'
From bc33b285d010b991c897da00365e62718ba5a82d Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Fri, 11 Nov 2022 18:38:13 -0500
Subject: [PATCH 11/91] use v1.9 env yml
---
env-r.yml | 776 +++++++++++++++++++++++++++---------------------------
env.yml | 511 ++++++++++++++++++-----------------
2 files changed, 634 insertions(+), 653 deletions(-)
diff --git a/env-r.yml b/env-r.yml
index a4fec770..4b30a89a 100644
--- a/env-r.yml
+++ b/env-r.yml
@@ -1,397 +1,387 @@
+name: null
channels:
- conda-forge
- bioconda
dependencies:
- - _libgcc_mutex=0.1
- - _openmp_mutex=4.5
- - _r-mutex=1.0.1
- - binutils_impl_linux-64=2.36.1
- - bioconductor-all=1.36.0
- - bioconductor-annotate=1.72.0
- - bioconductor-annotationdbi=1.56.1
- - bioconductor-annotationfilter=1.18.0
- - bioconductor-annotationhub=3.2.0
- - bioconductor-apeglm=1.16.0
- - bioconductor-biobase=2.54.0
- - bioconductor-biocfilecache=2.2.0
- - bioconductor-biocgenerics=0.40.0
- - bioconductor-biocio=1.4.0
- - bioconductor-biocparallel=1.28.0
- - bioconductor-biocversion=3.14.0
- - bioconductor-biomart=2.50.0
- - bioconductor-biostrings=2.62.0
- - bioconductor-clusterprofiler=4.2.0
- - bioconductor-complexheatmap=2.10.0
- - bioconductor-consensusclusterplus=1.58.0
- - bioconductor-degreport=1.30.0
- - bioconductor-delayedarray=0.20.0
- - bioconductor-deseq2=1.34.0
- - bioconductor-do.db=2.9
- - bioconductor-dose=3.20.0
- - bioconductor-dupradar=1.24.0
- - bioconductor-edger=3.36.0
- - bioconductor-enrichplot=1.14.1
- - bioconductor-ensembldb=2.18.1
- - bioconductor-fgsea=1.20.0
- - bioconductor-genefilter=1.76.0
- - bioconductor-geneplotter=1.72.0
- - bioconductor-genomeinfodb=1.30.0
- - bioconductor-genomeinfodbdata=1.2.7
- - bioconductor-genomicalignments=1.30.0
- - bioconductor-genomicfeatures=1.46.1
- - bioconductor-genomicranges=1.46.0
- - bioconductor-ggtree=3.2.0
- - bioconductor-go.db=3.14.0
- - bioconductor-gosemsim=2.20.0
- - bioconductor-graph=1.72.0
- - bioconductor-graphite=1.40.0
- - bioconductor-ihw=1.22.0
- - bioconductor-interactivedisplaybase=1.32.0
- - bioconductor-iranges=2.28.0
- - bioconductor-keggrest=1.34.0
- - bioconductor-limma=3.50.0
- - bioconductor-lpsymphony=1.22.0
- - bioconductor-matrixgenerics=1.6.0
- - bioconductor-protgenerics=1.26.0
- - bioconductor-qvalue=2.26.0
- - bioconductor-reactome.db=1.77.0
- - bioconductor-reactomepa=1.38.0
- - bioconductor-rhdf5=2.38.0
- - bioconductor-rhdf5filters=1.6.0
- - bioconductor-rhdf5lib=1.16.0
- - bioconductor-rhtslib=1.26.0
- - bioconductor-rsamtools=2.10.0
- - bioconductor-rsubread=2.8.0
- - bioconductor-rtracklayer=1.54.0
- - bioconductor-s4vectors=0.32.0
- - bioconductor-summarizedexperiment=1.24.0
- - bioconductor-sva=3.42.0
- - bioconductor-treeio=1.18.0
- - bioconductor-tximport=1.22.0
- - bioconductor-xvector=0.34.0
- - bioconductor-zlibbioc=1.40.0
- - bwidget=1.9.14
- - bzip2=1.0.8
- - c-ares=1.18.1
- - ca-certificates=2021.10.8
- - cairo=1.16.0
- - curl=7.83.1
- - expat=2.4.8
- - font-ttf-dejavu-sans-mono=2.37
- - font-ttf-inconsolata=3.000
- - font-ttf-source-code-pro=2.038
- - font-ttf-ubuntu=0.83
- - fontconfig=2.14.0
- - fonts-conda-ecosystem=1
- - fonts-conda-forge=1
- - freetype=2.10.4
- - fribidi=1.0.10
- - gcc_impl_linux-64=12.1.0
- - gettext=0.19.8.1
- - gfortran_impl_linux-64=12.1.0
- - gmp=6.2.1
- - graphite2=1.3.13
- - gsl=2.7
- - gxx_impl_linux-64=12.1.0
- - harfbuzz=5.1.0
- - icu=70.1
- - jpeg=9e
- - kernel-headers_linux-64=2.6.32
- - keyutils=1.6.1
- - krb5=1.19.3
- - ld_impl_linux-64=2.36.1
- - lerc=3.0
- - libblas=3.9.0
- - libcblas=3.9.0
- - libcurl=7.83.1
- - libdeflate=1.12
- - libedit=3.1.20191231
- - libev=4.33
- - libffi=3.4.2
- - libgcc-devel_linux-64=12.1.0
- - libgcc-ng=12.1.0
- - libgfortran-ng=12.1.0
- - libgfortran5=12.1.0
- - libgit2=1.3.0
- - libglib=2.72.1
- - libgomp=12.1.0
- - libiconv=1.16
- - liblapack=3.9.0
- - libnghttp2=1.47.0
- - libopenblas=0.3.21
- - libpng=1.6.38
- - libsanitizer=12.1.0
- - libssh2=1.10.0
- - libstdcxx-devel_linux-64=12.1.0
- - libstdcxx-ng=12.1.0
- - libtiff=4.4.0
- - libuuid=2.32.1
- - libwebp-base=1.2.1
- - libxcb=1.13
- - libxml2=2.9.14
- - libzlib=1.2.12
- - lz4-c=1.9.3
- - make=4.3
- - ncurses=6.3
- - openssl=1.1.1q
- - pandoc=2.16.1
- - pango=1.50.9
- - pcre=8.45
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- - pixman=0.40.0
- - pthread-stubs=0.4
- - r-ape=5.5
- - r-aplot=0.1.1
- - r-ashr=2.2_47
- - r-askpass=1.1
- - r-assertthat=0.2.1
- - r-babelgene=21.4
- - r-backports=1.3.0
- - r-base=4.1.3
- - r-base64enc=0.1_3
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- - r-clue=0.3_60
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- - r-dbplyr=2.1.1
- - r-dendextend=1.15.2
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- - r-foreach=1.5.1
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+ - sysroot_linux-64=2.12=he073ed8_15
+ - tk=8.6.12=h27826a3_0
+ - tktable=2.10=hb7b940f_3
+ - xorg-kbproto=1.0.7=h7f98852_1002
+ - xorg-libice=1.0.10=h7f98852_0
+ - xorg-libsm=1.2.3=hd9c2040_1000
+ - xorg-libx11=1.7.2=h7f98852_0
+ - xorg-libxau=1.0.9=h7f98852_0
+ - xorg-libxdmcp=1.1.3=h7f98852_0
+ - xorg-libxext=1.3.4=h7f98852_1
+ - xorg-libxrender=0.9.10=h7f98852_1003
+ - xorg-libxt=1.2.1=h7f98852_2
+ - xorg-renderproto=0.11.1=h7f98852_1002
+ - xorg-xextproto=7.3.0=h7f98852_1002
+ - xorg-xproto=7.0.31=h7f98852_1007
+ - xz=5.2.6=h166bdaf_0
+ - zlib=1.2.13=h166bdaf_4
+ - zstd=1.5.2=h6239696_4
+prefix: /home/dalerr/proj/lcdb-wf/env-r
diff --git a/env.yml b/env.yml
index f0b068e2..66a8bd01 100644
--- a/env.yml
+++ b/env.yml
@@ -1,312 +1,306 @@
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- _libgcc_mutex=0.1
- _openmp_mutex=4.5
- _r-mutex=1.0.1
- - aiohttp=3.7.4
- - alsa-lib=1.2.3
- - amply=0.1.4
- - apipkg=1.5
+ - alsa-lib=1.2.3.2
+ - amply=0.1.5
- appdirs=1.4.4
- - argcomplete=1.12.3
+ - argcomplete=2.0.0
- argh=0.26.2
- - async-timeout=3.0.1
- - attrs=20.3.0
- - azure-common=1.1.27
- - azure-core=1.12.0
- - azure-storage-blob=12.8.1
+ - asttokens=2.0.8
+ - attr=2.5.1
+ - attrs=22.1.0
- backcall=0.2.0
- backports=1.0
- backports.functools_lru_cache=1.6.4
- bedtools=2.30.0
- - binutils_impl_linux-64=2.35.1
- - binutils_linux-64=2.35
- - biopython=1.78
- - blinker=1.4
+ - binutils_impl_linux-64=2.39
+ - binutils_linux-64=2.39
+ - biopython=1.79
- boost-cpp=1.74.0
- - boto=2.49.0
- - boto3=1.17.56
- - botocore=1.20.57
- - bowtie=1.3.0
- - bowtie2=2.4.2
+ - bowtie=1.3.1
+ - bowtie2=2.5.0
+ - brotli=1.0.9
+ - brotli-bin=1.0.9
- brotlipy=0.7.0
- bwidget=1.9.14
- - bx-python=0.8.11
+ - bx-python=0.9.0
- bzip2=1.0.8
- - c-ares=1.17.1
- - ca-certificates=2021.4.13
- - cachetools=4.2.1
+ - c-ares=1.18.1
+ - ca-certificates=2022.9.24
- cairo=1.16.0
- - certifi=2020.12.5
- - cffi=1.14.5
- - chardet=4.0.0
- - click=7.1.2
- - coincbc=2.10.5
- - colorama=0.4.4
- - coloredlogs=15.0
+ - certifi=2022.9.24
+ - cffi=1.15.1
+ - charset-normalizer=2.1.1
+ - click=8.1.3
+ - coin-or-cbc=2.10.8
+ - coin-or-cgl=0.60.6
+ - coin-or-clp=1.17.7
+ - coin-or-osi=0.108.7
+ - coin-or-utils=2.11.6
+ - coincbc=2.10.8
+ - colorama=0.4.6
+ - coloredlogs=15.0.1
- colormath=3.0.0
- commonmark=0.9.1
- - configargparse=1.4
- - cryptography=3.4.7
- - curl=7.76.1
- - cutadapt=3.4
- - cycler=0.10.0
+ - configargparse=1.5.3
+ - connection_pool=0.0.3
+ - contourpy=1.0.6
+ - cryptography=38.0.2
+ - curl=7.86.0
+ - cutadapt=4.1
+ - cycler=0.11.0
+ - dataclasses=0.8
- datrie=0.8.2
- - dbus=1.13.18
- - decorator=5.0.7
+ - dbus=1.13.6
+ - decorator=5.1.1
- deeptools=3.5.1
- deeptoolsintervals=0.1.9
- - dnaio=0.5.0
- - docutils=0.17.1
- - execnet=1.8.0
- - expat=2.3.0
- - fastq-screen=0.14.0
+ - dnaio=0.9.1
+ - docutils=0.19
+ - dpath=2.0.6
+ - exceptiongroup=1.0.0
+ - execnet=1.9.0
+ - executing=1.1.1
+ - expat=2.5.0
+ - fastq-screen=0.15.2
- fastqc=0.11.9
- - filelock=3.0.12
+ - fftw=3.3.10
+ - filelock=3.8.0
- font-ttf-dejavu-sans-mono=2.37
- - fontconfig=2.13.1
- - freetype=2.10.4
+ - font-ttf-inconsolata=3.000
+ - font-ttf-source-code-pro=2.038
+ - font-ttf-ubuntu=0.83
+ - fontconfig=2.14.1
+ - fonts-conda-ecosystem=1
+ - fonts-conda-forge=1
+ - fonttools=4.38.0
+ - freetype=2.12.1
- fribidi=1.0.10
- future=0.18.2
- gat=1.3.6
- - gcc_impl_linux-64=9.3.0
- - gcc_linux-64=9.3.0
- - gettext=0.21.0
- - gffread=0.12.1
- - gffutils=0.10.1
- - gfortran_impl_linux-64=9.3.0
- - gfortran_linux-64=9.3.0
+ - gcc_impl_linux-64=10.4.0
+ - gcc_linux-64=10.4.0
+ - gettext=0.21.1
+ - gffread=0.12.7
+ - gffutils=0.11.1
+ - gfortran_impl_linux-64=10.4.0
+ - gfortran_linux-64=10.4.0
- giflib=5.2.1
- - gitdb=4.0.7
- - gitpython=3.1.15
- - glib=2.68.1
- - glib-tools=2.68.1
- - google-api-core=1.26.2
- - google-auth=1.29.0
- - google-cloud-core=1.6.0
- - google-cloud-storage=1.37.1
- - google-crc32c=1.1.2
- - google-resumable-media=1.2.0
- - googleapis-common-protos=1.53.0
- - graphite2=1.3.14
- - gsl=2.6
- - gst-plugins-base=1.18.4
- - gstreamer=1.18.4
- - gxx_impl_linux-64=9.3.0
- - gxx_linux-64=9.3.0
- - harfbuzz=2.8.0
- - hdf5=1.10.6
+ - gitdb=4.0.9
+ - gitpython=3.1.29
+ - glib=2.74.1
+ - glib-tools=2.74.1
+ - graphite2=1.3.13
+ - gsl=2.7
+ - gst-plugins-base=1.18.5
+ - gstreamer=1.20.3
+ - gxx_impl_linux-64=10.4.0
+ - gxx_linux-64=10.4.0
+ - harfbuzz=4.2.0
+ - hdf5=1.12.1
- hisat2=2.2.1
- - htslib=1.12
- - humanfriendly=9.1
- - icu=68.1
- - idna=2.10
- - importlib-metadata=4.0.1
- - importlib_metadata=4.0.1
+ - htslib=1.16
+ - humanfriendly=10.0
+ - icu=69.1
+ - idna=3.4
+ - importlib-metadata=4.11.4
+ - importlib_metadata=4.11.4
+ - importlib_resources=5.10.0
- iniconfig=1.1.1
- intervalstats=1.01
- - ipython=7.22.0
- - ipython_genutils=0.2.0
+ - ipython=8.6.0
- isa-l=2.30.0
- - isodate=0.6.0
- - jedi=0.18.0
- - jemalloc=5.2.1
- - jinja2=2.11.3
- - jmespath=0.10.0
- - jpeg=9d
- - jsonschema=3.2.0
- - jupyter_core=4.7.1
- - kallisto=0.46.2
+ - jack=1.9.18
+ - jedi=0.18.1
+ - jinja2=3.1.2
+ - jpeg=9e
+ - jsonschema=4.16.0
+ - jupyter_core=4.11.1
+ - kallisto=0.48.0
- kernel-headers_linux-64=2.6.32
- - kiwisolver=1.3.1
- - krb5=1.17.2
- - lcms2=2.12
- - ld_impl_linux-64=2.35.1
+ - keyutils=1.6.1
+ - kiwisolver=1.4.4
+ - krb5=1.19.3
+ - lcms2=2.13.1
+ - ld_impl_linux-64=2.39
+ - lerc=4.0.0
- libblas=3.9.0
+ - libbrotlicommon=1.0.9
+ - libbrotlidec=1.0.9
+ - libbrotlienc=1.0.9
+ - libcap=2.64
- libcblas=3.9.0
- - libclang=11.1.0
- - libcrc32c=1.1.1
- - libcurl=7.76.1
- - libdeflate=1.7
- - libedit=3.1.20210216
+ - libclang=13.0.1
+ - libcups=2.3.3
+ - libcurl=7.86.0
+ - libdb=6.2.32
+ - libdeflate=1.13
+ - libedit=3.1.20191231
- libev=4.33
- libevent=2.1.10
- - libffi=3.3
- - libgcc-devel_linux-64=9.3.0
- - libgcc-ng=9.3.0
- - libgd=2.3.2
- - libgfortran-ng=9.3.0
- - libgfortran5=9.3.0
- - libglib=2.68.1
- - libgomp=9.3.0
- - libiconv=1.16
+ - libffi=3.4.2
+ - libflac=1.3.4
+ - libgcc-devel_linux-64=10.4.0
+ - libgcc-ng=12.2.0
+ - libgd=2.3.3
+ - libgfortran-ng=12.2.0
+ - libgfortran5=12.2.0
+ - libglib=2.74.1
+ - libgomp=12.2.0
+ - libiconv=1.17
+ - libjemalloc=5.2.1
- liblapack=3.9.0
- - libllvm11=11.1.0
- - libnghttp2=1.43.0
- - libopenblas=0.3.13
- - libpng=1.6.37
- - libpq=13.2
- - libprotobuf=3.15.8
- - libssh2=1.9.0
- - libstdcxx-devel_linux-64=9.3.0
- - libstdcxx-ng=9.3.0
- - libtiff=4.2.0
+ - liblapacke=3.9.0
+ - libllvm13=13.0.1
+ - libnghttp2=1.47.0
+ - libnsl=2.0.0
+ - libogg=1.3.4
+ - libopenblas=0.3.21
+ - libopus=1.3.1
+ - libpng=1.6.38
+ - libpq=14.5
+ - libsanitizer=10.4.0
+ - libsndfile=1.0.31
+ - libsqlite=3.39.4
+ - libssh2=1.10.0
+ - libstdcxx-devel_linux-64=10.4.0
+ - libstdcxx-ng=12.2.0
+ - libtiff=4.4.0
+ - libtool=2.4.6
+ - libudev1=251
- libuuid=2.32.1
- - libwebp=1.2.0
- - libwebp-base=1.2.0
- - libxcb=1.14
+ - libvorbis=1.3.7
+ - libwebp=1.2.4
+ - libwebp-base=1.2.4
+ - libxcb=1.13
- libxkbcommon=1.0.3
- - libxml2=2.9.10
- - llvm-openmp=11.1.0
- - lz4-c=1.9.3
+ - libxml2=2.9.12
+ - libzlib=1.2.13
- lzo=2.10
- lzstring=1.0.4
- make=4.3
- - markdown=3.3.4
- - markupsafe=1.1.1
- - matplotlib=3.4.1
- - matplotlib-base=3.4.1
- - mkl=2020.4
- - more-itertools=8.7.0
- - msrest=0.6.21
- - multidict=5.1.0
- - multiqc=1.10.1
- - mysql-common=8.0.23
+ - markdown=3.4.1
+ - markupsafe=2.1.1
+ - matplotlib=3.6.0
+ - matplotlib-base=3.6.0
+ - matplotlib-inline=0.1.6
+ - multiqc=1.13
+ - munkres=1.1.4
+ - mysql-common=8.0.31
- mysql-connector-c=6.1.11
- - mysql-libs=8.0.23
- - nbformat=5.1.3
- - ncbi-ngs-sdk=2.11.0
- - ncurses=6.2
- - networkx=2.5
- - nspr=4.30
- - nss=3.64
- - numpy=1.20.2
- - oauthlib=3.1.0
- - olefile=0.46
- - openblas=0.3.13
- - openjdk=11.0.9.1
- - openssl=1.1.1k
- - packaging=20.9
- - pandas=1.2.4
- - pandoc=2.12
- - pango=1.48.4
- - parso=0.8.2
- - patsy=0.5.1
- - pcre=8.44
- - pcre2=10.36
- - perl=5.26.2
- - perl-app-cpanminus=1.7044
- - perl-business-isbn=3.004
- - perl-business-isbn-data=20140910.003
- - perl-carp=1.38
- - perl-constant=1.33
- - perl-data-dumper=2.173
- - perl-encode=2.88
- - perl-exporter=5.72
- - perl-extutils-makemaker=7.36
- - perl-file-path=2.16
- - perl-file-temp=0.2304
- - perl-gd=2.68
+ - mysql-libs=8.0.31
+ - nbformat=5.7.0
+ - ncurses=6.3
+ - networkx=2.8.7
+ - nspr=4.32
+ - nss=3.78
+ - numpy=1.23.4
+ - openjdk=11.0.1
+ - openjpeg=2.5.0
+ - openssl=1.1.1q
+ - packaging=21.3
+ - pandas=1.5.1
+ - pandoc=2.19.2
+ - pango=1.50.7
+ - parso=0.8.3
+ - patsy=0.5.3
+ - pbzip2=1.1.13
+ - pcre2=10.37
+ - perl=5.32.1
+ - perl-gd=2.76
- perl-gdgraph=1.54
- perl-gdtextutil=0.86
- - perl-mime-base64=3.15
- - perl-parent=0.236
- - perl-uri=1.76
- - perl-xml-libxml=2.0132
- - perl-xml-namespacesupport=1.12
- - perl-xml-sax=1.02
- - perl-xml-sax-base=1.09
- - perl-xsloader=0.24
- pexpect=4.8.0
- - picard=2.25.2
+ - picard=2.27.4
- pickleshare=0.7.5
- pigz=2.6
- - pillow=8.2.0
- - pip=21.0.1
+ - pillow=9.2.0
+ - pip=22.3
- pixman=0.40.0
- - plotly=4.14.3
- - pluggy=0.13.1
- - preseq=3.1.2
- - prompt-toolkit=3.0.18
- - protobuf=3.15.8
- - psutil=5.8.0
+ - pkgutil-resolve-name=1.3.10
+ - plac=1.3.5
+ - plotly=5.11.0
+ - pluggy=1.0.0
+ - preseq=3.2.0
+ - prompt-toolkit=3.0.31
+ - psutil=5.9.3
+ - pthread-stubs=0.4
- ptyprocess=0.7.0
- - pulp=2.4
- - py=1.10.0
+ - pulp=2.6.0
+ - pulseaudio=14.0
+ - pure_eval=0.2.2
- py2bit=0.3.0
- - pyasn1=0.4.8
- - pyasn1-modules=0.2.8
- - pybedtools=0.8.2
+ - pybedtools=0.9.0
- pybigwig=0.3.18
- - pycparser=2.20
- - pyfaidx=0.5.9.5
- - pygments=2.8.1
- - pyjwt=2.0.1
- - pyopenssl=20.0.1
- - pyparsing=2.4.7
- - pyqt=5.12.3
- - pyqt-impl=5.12.3
- - pyqt5-sip=4.19.18
- - pyqtchart=5.12
- - pyqtwebengine=5.12.1
- - pyrsistent=0.17.3
- - pysam=0.16.0.1
+ - pycparser=2.21
+ - pyfaidx=0.7.1
+ - pygments=2.13.0
+ - pyopenssl=22.1.0
+ - pyparsing=3.0.9
+ - pyqt=5.15.4
+ - pyqt5-sip=12.9.0
+ - pyrsistent=0.18.1
+ - pysam=0.19.1
- pysocks=1.7.1
- - pytest=6.2.3
- - pytest-forked=1.3.0
- - pytest-xdist=2.2.1
- - python=3.9.4
- - python-dateutil=2.8.1
- - python-isal=0.10.0
- - python-lzo=1.12
- - python_abi=3.9
- - pytz=2021.1
- - pyyaml=5.4.1
- - qt=5.12.9
- - r-base=4.0.3
+ - pytest=7.2.0
+ - pytest-xdist=3.0.2
+ - python=3.10.6
+ - python-dateutil=2.8.2
+ - python-fastjsonschema=2.16.2
+ - python-isal=1.1.0
+ - python-lzo=1.14
+ - python_abi=3.10
+ - pytz=2022.5
+ - pyvcf3=1.0.3
+ - pyyaml=6.0
+ - qt-main=5.15.2
+ - r-base=4.1.3
- ratelimiter=1.2.0
- - readline=8.1
- - requests=2.25.1
- - requests-oauthlib=1.3.0
- - retrying=1.3.3
- - rich=10.1.0
- - rsa=4.7.2
- - rseqc=4.0.0
- - s3transfer=0.4.2
- - salmon=1.4.0
- - samtools=1.12
- - scipy=1.6.2
- - seaborn=0.11.1
- - seaborn-base=0.11.1
+ - readline=8.1.2
+ - requests=2.28.1
+ - reretry=0.11.1
+ - rich=12.6.0
+ - rich-click=1.5.2
+ - rseqc=5.0.1
+ - salmon=1.9.0
+ - samtools=1.16.1
+ - scipy=1.9.3
+ - seaborn=0.12.1
+ - seaborn-base=0.12.1
- sed=4.8
- - setuptools=52.0.0
- - simplejson=3.17.2
- - six=1.15.0
- - smart_open=5.0.0
+ - setuptools=65.5.0
+ - simplejson=3.17.6
+ - sip=6.5.1
+ - six=1.16.0
+ - smart_open=6.2.0
- smmap=3.0.5
- - snakemake-minimal=6.2.1
+ - snakemake-minimal=7.17.1
- spectra=0.0.11
- - sqlite=3.35.5
- - sra-tools=2.10.0
- - star=2.7.8a
- - statsmodels=0.12.2
+ - sqlite=3.39.4
+ - sra-tools=2.9.6
+ - stack_data=0.5.1
+ - star=2.7.10a
+ - statsmodels=0.13.2
- stopit=1.1.2
- subread=2.0.1
- sysroot_linux-64=2.12
- - tbb=2020.3
- - tk=8.6.10
+ - tabulate=0.9.0
+ - tbb=2021.6.0
+ - tenacity=8.1.0
+ - tk=8.6.12
- tktable=2.10
- toml=0.10.2
- - toposort=1.6
- - tornado=6.1
+ - tomli=2.0.1
+ - toposort=1.7
+ - tornado=6.2
- trackhub=0.2.4
- - traitlets=5.0.5
- - typing-extensions=3.7.4.3
- - typing_extensions=3.7.4.3
- - tzdata=2021a
+ - traitlets=5.5.0
+ - typing_extensions=4.4.0
+ - tzdata=2022f
- ucsc-bedgraphtobigwig=377
- ucsc-bedsort=377
- ucsc-bedtobigbed=377
@@ -318,30 +312,27 @@ dependencies:
- ucsc-oligomatch=377
- ucsc-twobittofa=377
- ucsc-wigtobigwig=377
- - urllib3=1.26.4
+ - unicodedata2=15.0.0
+ - urllib3=1.26.11
- wcwidth=0.2.5
- - wheel=0.36.2
- - wrapt=1.12.1
- - xopen=1.1.0
- - xorg-fixesproto=5.0
- - xorg-inputproto=2.3.2
+ - wheel=0.37.1
+ - wrapt=1.14.1
+ - xopen=1.6.0
- xorg-kbproto=1.0.7
- xorg-libice=1.0.10
- xorg-libsm=1.2.3
- - xorg-libx11=1.6.12
+ - xorg-libx11=1.7.2
+ - xorg-libxau=1.0.9
+ - xorg-libxdmcp=1.1.3
- xorg-libxext=1.3.4
- - xorg-libxfixes=5.0.3
- - xorg-libxi=1.7.10
- xorg-libxrender=0.9.10
- xorg-libxt=1.2.1
- - xorg-libxtst=1.2.3
- - xorg-recordproto=1.14.2
- xorg-renderproto=0.11.1
- xorg-xextproto=7.3.0
- xorg-xproto=7.0.31
- - xz=5.2.5
+ - xz=5.2.6
- yaml=0.2.5
- - yarl=1.5.1
- - zipp=3.4.1
- - zlib=1.2.11
- - zstd=1.4.9
+ - yte=1.5.1
+ - zipp=3.10.0
+ - zlib=1.2.13
+ - zstd=1.5.2
From 1748d992f42e6e6230ea21ce59552b77783982dc Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov`>
Date: Sat, 12 Nov 2022 09:07:00 -0500
Subject: [PATCH 12/91] update conda config; hash on env-r
---
.github/workflows/main.yaml | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
index 062fec00..5ce27779 100644
--- a/.github/workflows/main.yaml
+++ b/.github/workflows/main.yaml
@@ -13,7 +13,7 @@ jobs:
uses: actions/cache@v1
with:
path: /opt/conda
- key: ${{ hashFiles('env.yml') }}
+ key: ${{ hashFiles('env.yml') }}-${{ hashFiles('env-r.yml') }}
- name: Rebuild cache
if: steps.cache-conda.outputs.cache-hit != 'true'
@@ -21,6 +21,8 @@ jobs:
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
+ conda config --set channel_priority strict
+
conda install mamba -y
mamba env create -n lcdb-wf-test --file env.yml
mamba env create -n lcdb-wf-test-r --file env-r.yml
From 9daee34bf6d0128664191a7f44a9f9b357ef6c76 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov`>
Date: Sat, 12 Nov 2022 09:09:03 -0500
Subject: [PATCH 13/91] update cache action to v3
---
.github/workflows/main.yaml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
index 5ce27779..eea6b2e9 100644
--- a/.github/workflows/main.yaml
+++ b/.github/workflows/main.yaml
@@ -10,7 +10,7 @@ jobs:
- name: Cache conda env
id: cache-conda
- uses: actions/cache@v1
+ uses: actions/cache@v3
with:
path: /opt/conda
key: ${{ hashFiles('env.yml') }}-${{ hashFiles('env-r.yml') }}
From 85b7951cdc73d4fc0cb09694bb141a732fd0fc12 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov`>
Date: Sat, 12 Nov 2022 09:11:23 -0500
Subject: [PATCH 14/91] github actions fail fast
---
.github/workflows/main.yaml | 2 ++
1 file changed, 2 insertions(+)
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
index eea6b2e9..9d4581eb 100644
--- a/.github/workflows/main.yaml
+++ b/.github/workflows/main.yaml
@@ -3,6 +3,8 @@ jobs:
build:
runs-on: ubuntu-latest
+ strategy:
+ fail-fast: true
container: continuumio/miniconda3
steps:
From cd7e6b0b6967bcf97e4be7ceed80c0ad75f90b61 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov`>
Date: Sat, 19 Nov 2022 14:42:21 -0500
Subject: [PATCH 15/91] add gres=lscratch to clusterconfig and wrapper_slurm
This is because recent versions of Snakemake use tempdir, so everything
(including the main process) needs to use it as well.
---
include/WRAPPER_SLURM | 1 +
workflows/rnaseq/config/clusterconfig.yaml | 12 ++++++------
2 files changed, 7 insertions(+), 6 deletions(-)
diff --git a/include/WRAPPER_SLURM b/include/WRAPPER_SLURM
index 548f6afb..bed1df6d 100755
--- a/include/WRAPPER_SLURM
+++ b/include/WRAPPER_SLURM
@@ -2,6 +2,7 @@
#SBATCH --job-name="lcdb-wf"
#SBATCH --partition="norm"
#SBATCH --time=12:00:00
+#SBATHC --gres=lscratch:5
# make logdir
if [[ ! -e logs ]]; then mkdir -p logs; fi
diff --git a/workflows/rnaseq/config/clusterconfig.yaml b/workflows/rnaseq/config/clusterconfig.yaml
index f002fffd..e71837e1 100644
--- a/workflows/rnaseq/config/clusterconfig.yaml
+++ b/workflows/rnaseq/config/clusterconfig.yaml
@@ -20,16 +20,16 @@ collectrnaseqmetrics:
prefix: "--gres=lscratch:20 --time=4:00:00 --mem=32g --partition=quick"
salmon_index:
- prefix: "--mem=32g"
+ prefix: "--gres=lscratch:20 --mem=32g"
salmon:
- prefix: "--mem=32g"
+ prefix: "--gres=lscratch:20 --mem=32g"
kallisto_index:
- prefix: "--mem=32g"
+ prefix: "--gres=lscratch:20 --mem=32g"
kallisto:
- prefix: "--mem=32g"
+ prefix: "--gres=lscratch:20 --mem=32g"
bigwig_neg:
prefix: "--gres=lscratch:20 --mem=16g"
@@ -38,7 +38,7 @@ bigwig_pos:
prefix: "--gres=lscratch:20 --mem=16g"
star:
- prefix: "--time=8:00:00 --mem=64g"
+ prefix: "--gres=lscratch:20 --time=8:00:00 --mem=64g"
star_index:
- prefix: "--time=8:00:00 --mem=64g"
+ prefix: "--gres=lscratch:20 --time=8:00:00 --mem=64g"
From 1f4782461f9436717c9e5d8217a30e1c5ef31885 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov`>
Date: Sat, 19 Nov 2022 14:47:43 -0500
Subject: [PATCH 16/91] fix #368
---
lib/common.py | 3 +++
1 file changed, 3 insertions(+)
diff --git a/lib/common.py b/lib/common.py
index 24b7e95c..79d43187 100644
--- a/lib/common.py
+++ b/lib/common.py
@@ -629,6 +629,9 @@ def load_config(config, missing_references_ok=False):
# Here we populate a list of reference sections. Items later on the list
# will have higher priority
includes = config.get('include_references', [])
+ for i in includes:
+ if not os.path.exists(i):
+ raise ValueError("include_references: '{}' does not exist".format(i))
reference_sections = []
# First the directories. Directories that come earlier lose to those that
From 172c4147a5f1c6040f1ecd34e49c4997b2309db3 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov`>
Date: Sat, 19 Nov 2022 15:01:40 -0500
Subject: [PATCH 17/91] fix #367
Detects SRA sampletables and raises exeception if "Layout" or "layout"
column not found.
---
lib/common.py | 15 +++++++++++++++
1 file changed, 15 insertions(+)
diff --git a/lib/common.py b/lib/common.py
index 79d43187..829cc129 100644
--- a/lib/common.py
+++ b/lib/common.py
@@ -719,6 +719,21 @@ def is_paired_end(sampletable, sample):
sample : str
Assumed to be found in the first column of `sampletable`
"""
+ # We can't fall back to detecting PE based on two fastq files provided for
+ # each sample when it's an SRA sampletable (which only has SRR accessions).
+ #
+ # So detect first detect if SRA sampletable based on presence of "Run"
+ # column and all values of that column starting with "SRR", and then raise
+ # an error if the Layout column does not exist.
+
+ if "Run" in sampletable.columns:
+ if all(sampletable["Run"].str.startswith("SRR")):
+ if "Layout" not in sampletable.columns and "layout" not in sampletable.columns:
+ raise ValueError(
+ "Sampletable appears to be SRA, but no 'Layout' column "
+ "found. This is required to specify single- or paired-end "
+ "libraries.")
+
row = sampletable.set_index(sampletable.columns[0]).loc[sample]
if 'orig_filename_R2' in row:
return True
From 98f420a8d5db3d076a1fdda6cfaacb78a03f6d09 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov`>
Date: Sat, 19 Nov 2022 15:08:17 -0500
Subject: [PATCH 18/91] add .bai to patterns/targets for markduplicates; fix
#351
This ensures it's always created, even if bigwigs are not created (which
otherwise cause them to enter the DAG)
---
workflows/chipseq/config/chipseq_patterns.yaml | 1 +
workflows/rnaseq/config/rnaseq_patterns.yaml | 1 +
2 files changed, 2 insertions(+)
diff --git a/workflows/chipseq/config/chipseq_patterns.yaml b/workflows/chipseq/config/chipseq_patterns.yaml
index c93562f2..84d59520 100644
--- a/workflows/chipseq/config/chipseq_patterns.yaml
+++ b/workflows/chipseq/config/chipseq_patterns.yaml
@@ -24,6 +24,7 @@ patterns_by_sample:
markduplicates:
bam: 'data/chipseq_samples/{sample}/{sample}.cutadapt.unique.nodups.bam'
+ bai: 'data/chipseq_samples/{sample}/{sample}.cutadapt.unique.nodups.bam.bai'
metrics: 'data/chipseq_samples/{sample}/{sample}.cutadapt.unique.nodups.bam.metrics'
merged_techreps: 'data/chipseq_merged/{label}/{label}.cutadapt.unique.nodups.merged.bam'
diff --git a/workflows/rnaseq/config/rnaseq_patterns.yaml b/workflows/rnaseq/config/rnaseq_patterns.yaml
index ecd95d7d..e7a6bdd1 100644
--- a/workflows/rnaseq/config/rnaseq_patterns.yaml
+++ b/workflows/rnaseq/config/rnaseq_patterns.yaml
@@ -25,6 +25,7 @@ rrna:
multiqc: 'data/rnaseq_aggregation/multiqc.html'
markduplicates:
bam: 'data/rnaseq_samples/{sample}/{sample}.cutadapt.markdups.bam'
+ bai: 'data/rnaseq_samples/{sample}/{sample}.cutadapt.markdups.bam.bai'
metrics: 'data/rnaseq_samples/{sample}/{sample}.cutadapt.markdups.bam.metrics'
collectrnaseqmetrics:
metrics: 'data/rnaseq_samples/{sample}/{sample}.collectrnaseqmetrics.metrics'
From 85be804a55a247c4c425afface048f955839c8f1 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov`>
Date: Sat, 19 Nov 2022 17:05:58 -0500
Subject: [PATCH 19/91] fix R tests
- use fully-qualified `:::` for accessing lcdbwf pkg functions
- fix function and argument names in tests
---
lib/lcdbwf/DESCRIPTION | 2 +-
lib/lcdbwf/R/loading.R | 2 +-
lib/lcdbwf/tests/testthat/test-dds.R | 6 +++---
lib/lcdbwf/tests/testthat/test-helpers.R | 4 ++--
lib/lcdbwf/tests/testthat/test-loading.R | 12 ++++++------
5 files changed, 13 insertions(+), 13 deletions(-)
diff --git a/lib/lcdbwf/DESCRIPTION b/lib/lcdbwf/DESCRIPTION
index d6781bb2..97dc6126 100644
--- a/lib/lcdbwf/DESCRIPTION
+++ b/lib/lcdbwf/DESCRIPTION
@@ -23,4 +23,4 @@ License: MIT
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.1
diff --git a/lib/lcdbwf/R/loading.R b/lib/lcdbwf/R/loading.R
index 06422033..9ff0eae1 100644
--- a/lib/lcdbwf/R/loading.R
+++ b/lib/lcdbwf/R/loading.R
@@ -19,7 +19,7 @@
#' Additional args are passed to DESeq2::DESeqDataSetFromMatrix.
DESeqDataSetFromCombinedFeatureCounts <- function(filename, sampletable,
design,
- sample_func=lcdbwf.samplename,
+ sample_func=lcdbwf_samplename,
subset_counts=FALSE, ...){
# The sampletable may be data.frame or tibble; if it's a tibble then it
diff --git a/lib/lcdbwf/tests/testthat/test-dds.R b/lib/lcdbwf/tests/testthat/test-dds.R
index a9043b3b..64f2da7f 100644
--- a/lib/lcdbwf/tests/testthat/test-dds.R
+++ b/lib/lcdbwf/tests/testthat/test-dds.R
@@ -5,13 +5,13 @@ test_that("stripping gene versions", {
rownames(dds) <- paste(rownames(dds), seq(1000), sep='.')
- expect_error(lcdbwf::strip_dotted_version_from_dds(dds), "Gene names don't appear to be Ensembl")
+ expect_error(lcdbwf:::strip_dotted_version_from_dds(dds), "Gene names don't appear to be Ensembl")
- forced <- lcdbwf::strip_dotted_version_from_dds(dds, force=TRUE)
+ forced <- lcdbwf:::strip_dotted_version_from_dds(dds, force=TRUE)
expect_equal(rownames(forced)[1], "gene1")
rownames(dds) <- paste0("ENS", rownames(dds), '.', seq(1000))
- fixed <- lcdbwf::strip_dotted_version_from_dds(dds)
+ fixed <- lcdbwf:::strip_dotted_version_from_dds(dds)
expect_equal(rownames(fixed)[1], "ENSgene1")
})
diff --git a/lib/lcdbwf/tests/testthat/test-helpers.R b/lib/lcdbwf/tests/testthat/test-helpers.R
index 491fc605..9938cf8f 100644
--- a/lib/lcdbwf/tests/testthat/test-helpers.R
+++ b/lib/lcdbwf/tests/testthat/test-helpers.R
@@ -532,8 +532,8 @@ res <- new("DESeqResults", priorInfo = list(), rownames = c("FBgn0000061",
lfcThreshold = 0))
-test_that("lcdbwf.samplename works", {
- res <- lcdbwf.samplename("data/rnaseq_samples/sampleNNN.cutadapt.bam")
+test_that("lcdbwf_samplename works", {
+ res <- lcdbwf_samplename("data/rnaseq_samples/sampleNNN.cutadapt.bam")
expect_equal(res, "sampleNNN")
})
diff --git a/lib/lcdbwf/tests/testthat/test-loading.R b/lib/lcdbwf/tests/testthat/test-loading.R
index 762813c5..9611d676 100644
--- a/lib/lcdbwf/tests/testthat/test-loading.R
+++ b/lib/lcdbwf/tests/testthat/test-loading.R
@@ -5,7 +5,7 @@ sampletable <- data.frame(
test_that("load from combined featurecounts", {
- dds <- lcdbwf::DESeqDataSetFromCombinedFeatureCounts(
+ dds <- lcdbwf:::DESeqDataSetFromCombinedFeatureCounts(
"featurecounts.txt",
sampletable,
design=~group
@@ -15,7 +15,7 @@ test_that("load from combined featurecounts", {
test_that("load from combined featurecounts, subset sampletable, no subset.counts", {
expect_error(
- lcdbwf::DESeqDataSetFromCombinedFeatureCounts(
+ lcdbwf:::DESeqDataSetFromCombinedFeatureCounts(
"featurecounts.txt",
sampletable %>% dplyr::filter(samplename != "sample4"),
design=~group),
@@ -27,10 +27,10 @@ test_that("load from combined featurecounts, subset sampletable, no subset.count
})
test_that("load from combined featurecounts, subset sampletable, with subset.counts", {
- dds <- lcdbwf::DESeqDataSetFromCombinedFeatureCounts(
+ dds <- lcdbwf:::DESeqDataSetFromCombinedFeatureCounts(
"featurecounts.txt",
sampletable %>% dplyr::filter(samplename != "sample4"),
- design=~group, subset.counts=TRUE)
+ design=~group, subset_counts=TRUE)
expect_s4_class(dds, "DESeqDataSet")
})
@@ -47,10 +47,10 @@ test_that("load from combined featurecounts, using custom func", {
stringr::str_split(stringr::fixed('/'), simplify=TRUE)
x[,1]
}
- dds <- lcdbwf::DESeqDataSetFromCombinedFeatureCounts(
+ dds <- lcdbwf:::DESeqDataSetFromCombinedFeatureCounts(
"featurecounts.txt",
sampletable2,
- sample.func=custom.func,
+ sample_func=custom.func,
design=~group)
expect_s4_class(dds, "DESeqDataSet")
From 43d8d8e0d4f58f636d67e1a260a6ad6bc5b0e9be Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov`>
Date: Sat, 19 Nov 2022 17:42:44 -0500
Subject: [PATCH 20/91] add test settings to bam coverage args
---
workflows/rnaseq/Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/workflows/rnaseq/Snakefile b/workflows/rnaseq/Snakefile
index 29d5af4a..e086402d 100644
--- a/workflows/rnaseq/Snakefile
+++ b/workflows/rnaseq/Snakefile
@@ -921,7 +921,7 @@ rule rseqc_read_distribution:
BAMCOVERAGE_ARGS = (
'--minMappingQuality 20 ' # excludes multimappers
'--smoothLength 10 ' # smooth signal with specified window
- '--normalizeUsing BPM ' # equivalent to TPM
+ # '--normalizeUsing BPM ' # equivalent to TPM # [TEST SETTINGS]
)
rule bigwig_neg:
From ea937ac962dc64117782370d042b87e3149ac4cc Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov`>
Date: Sat, 19 Nov 2022 17:47:29 -0500
Subject: [PATCH 21/91] initial move to using the lcdb-wf-test script for CI
---
.circleci/config.yml | 7 +-
test/lcdb-wf-test | 170 +++++++++++++++++++++++++++++++++++++++++++
2 files changed, 175 insertions(+), 2 deletions(-)
create mode 100755 test/lcdb-wf-test
diff --git a/.circleci/config.yml b/.circleci/config.yml
index c5ab1074..4a67bf43 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -98,6 +98,8 @@ variables:
cp workflows/colocalization/run_test.sh $DEPLOY/workflows/references
cp workflows/colocalization/run_test.sh $DEPLOY/workflows/colocalization
mkdir $DEPLOY/ci
+ mkdir $DEPLOY/test
+ cp test/lcdb-wf-test $DEPLOY/test
cp ci/get-data.py $DEPLOY/ci
# the ./run_test.sh scripts run this
@@ -105,7 +107,7 @@ variables:
# download example data
cd $DEPLOY
- python ci/get-data.py
+ test/lcdb-wf-test --get-data --kinds all
# --------------------------------------------------------------------------
# Run the doctests across the included modules
@@ -137,7 +139,8 @@ variables:
command: |
cd $DEPLOY/workflows/rnaseq
source activate lcdb-wf-test
- ./run_test.sh --use-conda -n
+ $DEPLOY/test/lcdb-wf-test --rnaseq dryrun
+
# --------------------------------------------------------------------------
# Standard chipseq workflow
chipseq-step: &chipseq-step
diff --git a/test/lcdb-wf-test b/test/lcdb-wf-test
new file mode 100755
index 00000000..18e4664a
--- /dev/null
+++ b/test/lcdb-wf-test
@@ -0,0 +1,170 @@
+#!/usr/bin/env python
+
+"""
+This script aims to make it more convenient to run various tests using
+different configs.
+"""
+import os
+import subprocess as sp
+import sys
+from pathlib import Path
+
+HERE = Path(__file__).resolve().parent
+TOPLEVEL = Path(__file__).resolve().parent.parent
+
+
+def get_data(kinds="all", branch="master", verbose=True):
+ """
+ Download the test data from the lcdb-test-data repo
+ """
+ URL = "https://github.com/lcdb/lcdb-test-data/blob/{0}/data/{{}}?raw=true".format(
+ branch
+ )
+ data_files = {
+ "rnaseq": [
+ (
+ "rnaseq_samples/sample1/sample1.small_R1.fastq.gz",
+ "workflows/rnaseq/data/example_data/rnaseq_sample1.fq.gz",
+ ),
+ (
+ "rnaseq_samples/sample2/sample2.small_R1.fastq.gz",
+ "workflows/rnaseq/data/example_data/rnaseq_sample2.fq.gz",
+ ),
+ (
+ "rnaseq_samples/sample3/sample3.small_R1.fastq.gz",
+ "workflows/rnaseq/data/example_data/rnaseq_sample3.fq.gz",
+ ),
+ (
+ "rnaseq_samples/sample4/sample4.small_R1.fastq.gz",
+ "workflows/rnaseq/data/example_data/rnaseq_sample4.fq.gz",
+ ),
+ (
+ "rnaseq_samples/sample1/sample1.small_R1.fastq.gz",
+ "workflows/rnaseq/data/example_data/rnaseq_sample1PE_1.fq.gz",
+ ),
+ (
+ "rnaseq_samples/sample1/sample1.small_R2.fastq.gz",
+ "workflows/rnaseq/data/example_data/rnaseq_sample1PE_2.fq.gz",
+ ),
+ (
+ "rnaseq_samples/sample2/sample2.small_R1.fastq.gz",
+ "workflows/rnaseq/data/example_data/rnaseq_sample2PE_1.fq.gz",
+ ),
+ (
+ "rnaseq_samples/sample2/sample2.small_R2.fastq.gz",
+ "workflows/rnaseq/data/example_data/rnaseq_sample2PE_2.fq.gz",
+ ),
+ ],
+ "chipseq": [
+ (
+ "chipseq_samples/input_1/input_1.tiny_R1.fastq.gz",
+ "workflows/chipseq/data/example_data/chipseq_input1.fq.gz",
+ ),
+ (
+ "chipseq_samples/input_2/input_2.tiny_R1.fastq.gz",
+ "workflows/chipseq/data/example_data/chipseq_input2.fq.gz",
+ ),
+ (
+ "chipseq_samples/input_3/input_3.tiny_R1.fastq.gz",
+ "workflows/chipseq/data/example_data/chipseq_input3.fq.gz",
+ ),
+ (
+ "chipseq_samples/ip_1/ip_1.tiny_R1.fastq.gz",
+ "workflows/chipseq/data/example_data/chipseq_ip1.fq.gz",
+ ),
+ (
+ "chipseq_samples/ip_2/ip_2.tiny_R1.fastq.gz",
+ "workflows/chipseq/data/example_data/chipseq_ip2.fq.gz",
+ ),
+ (
+ "chipseq_samples/ip_3/ip_3.tiny_R1.fastq.gz",
+ "workflows/chipseq/data/example_data/chipseq_ip3.fq.gz",
+ ),
+ (
+ "chipseq_samples/ip_4/ip_4.tiny_R1.fastq.gz",
+ "workflows/chipseq/data/example_data/chipseq_ip4.fq.gz",
+ ),
+ ],
+ }
+ cwd = os.getcwd()
+ if str(cwd) != str(TOPLEVEL):
+ raise ValueError(f"cwd: {cwd}; Please run this from the top level of the repo")
+ if kinds == "all":
+ kinds = list(data_files.keys())
+ for kind in kinds:
+ for fn, dest in data_files[kind]:
+ url = URL.format(fn)
+ if verbose:
+ print(f"downloading {url}")
+ if dest is None:
+ dest = fn
+ dest = Path(dest)
+ dest.parent.mkdir(parents=True, exist_ok=True)
+ sp.run(f"wget -q -O- {url} > {dest}", shell=True, check=True)
+
+def run_pytest():
+ sp.run(["pytest", "--doctest-modules", "lib"], check=True)
+
+def run_url_check():
+ sys.path.insert(0, str(TOPLEVEL))
+ from lib.common import check_all_urls_found
+ check_all_urls_found()
+
+def r_package_check(env_r='./env-r'):
+ sp.run([f"{env_r}/bin/Rscript", "-e", "testthat::test('lib/lcdbwf', export_all=TRUE)"])
+
+def snakefile(directory, args=None):
+ sp.run(['bash', 'run_test.sh'] + args, cwd=TOPLEVEL / directory, check=True)
+
+
+if __name__ == "__main__":
+
+ import argparse
+
+ ap = argparse.ArgumentParser()
+ ap.add_argument(
+ "--get-data",
+ action="store_true",
+ help="Download example data. See --kinds argument for controlling this",
+ )
+ ap.add_argument(
+ "--kinds",
+ nargs="+",
+ default="all",
+ choices=["chipseq", "rnaseq", "all"],
+ help="Download data for which workflows?"
+ )
+
+
+ ap.add_argument('--env', default='./env', help="Specify main conda env. Default is %(default)s")
+ ap.add_argument('--env-r', default='./env-r', help="Specify R conda env. Default is %(default)s")
+ ap.add_argument('--pytest', action='store_true', help="Run pytest unit tests on lib directory")
+ ap.add_argument('--urls', action='store_true', help='Check all URLs found across config files')
+ ap.add_argument('--r-test', action='store_true', help='Run devtools::test on lcdbwf R package. Set R environment with --env-r.')
+ ap.add_argument('--rnaseq', choices=['dryrun', 'standard'])
+ ap.add_argument('--references', action='store_true')
+ ap.add_argument('--cpus', help='Number of cores to use when calling snakemake, default is %(default)s', default='2')
+ args = ap.parse_args()
+ if args.get_data:
+ get_data(kinds=args.kinds)
+
+ if args.pytest:
+ run_pytest()
+
+ if args.urls:
+ run_url_check()
+
+ if args.r_test:
+ r_package_check()
+
+ if args.rnaseq:
+ if args.rnaseq == 'dryrun':
+ snakefile('workflows/rnaseq', ['-n', '--use-conda'])
+
+ if args.rnaseq == 'standard':
+ snakefile('workflows/rnaseq', ['--use-conda', '-j', args.cpus, '-k', '-p', '-r'])
+ sp.run(['python', 'rnaseq_trackhub.py', 'config/config.yaml', 'config/hub_config.yaml'], check=True, cwd='workflows/rnaseq')
+
+ if args.references:
+ snakefile('workflows/references', ['--use-conda', '-j', args.cpus, '-k', '-p', '-r', '--configfile', 'config/config.yaml'])
+# vim: ft=python
From 0e239d6966e25e3a0f6e18c4e4f795e54df7065f Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov`>
Date: Sat, 19 Nov 2022 17:56:24 -0500
Subject: [PATCH 22/91] fix "kinds" arg
---
test/lcdb-wf-test | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/test/lcdb-wf-test b/test/lcdb-wf-test
index 18e4664a..2c6e3633 100755
--- a/test/lcdb-wf-test
+++ b/test/lcdb-wf-test
@@ -89,7 +89,7 @@ def get_data(kinds="all", branch="master", verbose=True):
cwd = os.getcwd()
if str(cwd) != str(TOPLEVEL):
raise ValueError(f"cwd: {cwd}; Please run this from the top level of the repo")
- if kinds == "all":
+ if "all" in kinds:
kinds = list(data_files.keys())
for kind in kinds:
for fn, dest in data_files[kind]:
From ab28a1f6ce7c9b16f0a2a8c66ae8b9aeaf900fae Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov`>
Date: Sat, 19 Nov 2022 18:06:11 -0500
Subject: [PATCH 23/91] start v1.10 changelog
---
docs/changelog.rst | 12 ++++++++++++
1 file changed, 12 insertions(+)
diff --git a/docs/changelog.rst b/docs/changelog.rst
index e1fb489d..160bba54 100644
--- a/docs/changelog.rst
+++ b/docs/changelog.rst
@@ -1,5 +1,17 @@
Changelog
=========
+v1.10
+-----
+
+General
+~~~~~~~
+- Migrated to a unified testing script that simplifies local and CI testing
+- Added "--gres:lscratch" to all slurm-related params
+- If sampletable is from SRA, raise an error if a Layout column can't be found
+ (to prevent incorrect interpretation of samples as single-end)
+- Fix R tests
+- ensure bam indexes are made for the markdups bams, even if bigwigs are not created
+- fix library loads in rnaseq.Rmd to ensure they come before parallelization configuration
v1.9
----
From 7d39e803f093f1ef61f064a07e979bea2edcab9c Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Tue, 22 Nov 2022 20:03:22 -0500
Subject: [PATCH 24/91] next round of porting all tests to test/lcdb-wf-test
---
.circleci/config.yml | 95 +---
ci/ensure_docs.py | 4 +
test/lcdb-wf-test | 451 ++++++++++++------
test/test_configs/star_1pass.tsv | 3 +
test/test_configs/star_2pass.tsv | 3 +
.../test_sra_sampletable_SE_only.tsv | 6 +-
test/test_configs/two_samples.tsv | 4 +-
test/workflow_test_params.yaml | 61 +++
workflows/rnaseq/run_downstream_test.sh | 8 +
9 files changed, 422 insertions(+), 213 deletions(-)
mode change 100644 => 100755 ci/ensure_docs.py
create mode 100644 test/test_configs/star_1pass.tsv
create mode 100644 test/test_configs/star_2pass.tsv
create mode 100644 test/workflow_test_params.yaml
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 4a67bf43..b1a63dc1 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -107,7 +107,7 @@ variables:
# download example data
cd $DEPLOY
- test/lcdb-wf-test --get-data --kinds all
+ test/lcdb-wf-test data --kinds=all --verbose
# --------------------------------------------------------------------------
# Run the doctests across the included modules
@@ -117,17 +117,17 @@ variables:
command: |
source activate lcdb-wf-test
- # Ensure that the chunks in rnaseq.Rmd have matching documentation
- (cd ci && python ensure_docs.py)
+ # run unit tests and doctests for the modules in lib
+ test/lcdb-wf-test unit_tests --pytest
- pytest --doctest-modules lib
+ # Ensure that the chunks in rnaseq.Rmd have matching documentation
+ test/lcdb-wf-test unit_tests --ensure-docs
# find all URLs in reference configs and make sure they exist
- python -c 'from lib.common import check_all_urls_found; check_all_urls_found()'
+ test/lcdb-wf-test unit_tests --url-check
- source deactivate
- source activate lcdb-wf-test-r
- Rscript -e "devtools::test('lib/lcdbwf')"
+ # run R package unit tests using the R env
+ test/lcdb-wf-test unit_tests --r-test --env-r lcdb-wf-test-r
# --------------------------------------------------------------------------
@@ -137,7 +137,6 @@ variables:
run:
name: dry run
command: |
- cd $DEPLOY/workflows/rnaseq
source activate lcdb-wf-test
$DEPLOY/test/lcdb-wf-test --rnaseq dryrun
@@ -190,27 +189,29 @@ variables:
command: |
cd $DEPLOY/workflows/references
source activate lcdb-wf-test
- ./run_test.sh --use-conda -j2 -k -p -r --configfile config/config.yaml
+ $DEPLOY/test/lcdb-wf-test --references
+
# --------------------------------------------------------------------------
# Standard RNA-seq workflow
rnaseq-step: &rnaseq-step
run:
name: rnaseq workflow
command: |
- cd $DEPLOY/workflows/rnaseq
+ cd $DEPLOY
source activate lcdb-wf-test
- ./run_test.sh --use-conda -j2 -k -p -r
- python rnaseq_trackhub.py config/config.yaml config/hub_config.yaml
+ $DEPLOY/test/lcdb-wf-test rnaseq --run-workflow --use-conda -j2 -k -p -r
+
+ $DEPLOY/test/lcdb-wf-test rnaseq --trackhub
# Starting in v1.6, we separate out the non-R from the
# R environments. So we need to test the rnaseq.Rmd separately
# outside the context of the Snakefile.
source activate lcdb-wf-test-r
- # This script runs the preprocessor on the Rmd files and stores them
+ # This run the preprocessor on the Rmd files and stores them
# in a new download-test directory (see the comments in the script
# for details)
- bash run_downstream_test.sh
+ $DEPLOY/ test/lcdb-wf-test rnaseq --downstream
# bundle up the entire directory to be used as an artifact
tar -zcf downstream.tar.gz downstream-test/
@@ -224,63 +225,17 @@ variables:
command: |
ORIG=$(pwd)
cd $DEPLOY
- cp -r workflows/rnaseq workflows/rnaseq-misc-test
-
- # make a copy of the data so we can get a fresh copy each time below
- cp -r workflows/rnaseq/data /tmp/data
- cd workflows/rnaseq-misc-test
source activate lcdb-wf-test
- echo "test SRA, PE"
- rm -r data
- ./run_test.sh -j 1 --use-conda -k -p -r --until cutadapt \
- --configfile $ORIG/test/test_configs/test_rnaseq_config.yaml \
- --config sampletable=$ORIG/test/test_configs/test_sra_sampletable.tsv
-
- echo "test SRA, SE"
- rm -r data
- ./run_test.sh -j 1 --use-conda -k -p -r --until cutadapt \
- --configfile $ORIG/test/test_configs/test_rnaseq_config.yaml \
- --config sampletable=$ORIG/test/test_configs/test_sra_sampletable_SE_only.tsv
-
- echo "test strandedness, PE"
- rm -r data && cp -r /tmp/data data
- ./run_test.sh -j 2 --use-conda -k -p -r --until strand_check \
- --configfile $ORIG/test/test_configs/test_rnaseq_config.yaml \
- --config sampletable=$ORIG/test/test_configs/test_pe_sampletable.tsv
-
- echo "test strandedness, SE"
- rm -r data && cp -r /tmp/data data
- ./run_test.sh -j 2 --use-conda -k -p -r --until strand_check \
- --configfile $ORIG/test/test_configs/test_rnaseq_config.yaml \
- --config sampletable=$ORIG/test/test_configs/two_samples.tsv
-
- echo "test STAR 2-pass alignment"
- rm -r data && cp -r /tmp/data data
- ./run_test.sh -j 2 --use-conda -k -p -r \
- --forcerun star_pass1 \
- --configfile \
- $ORIG/test/test_configs/test_rnaseq_config.yaml \
- $ORIG/test/test_configs/star_override_2pass.yaml \
- --config sampletable=$ORIG/test/test_configs/two_samples.tsv \
- --until star_pass2
-
- echo "test STAR 1-pass alignment"
- rm -r data && cp -r /tmp/data data
- ./run_test.sh -j 2 --use-conda -k -p -r \
- --forcerun star \
- --configfile \
- $ORIG/test/test_configs/test_rnaseq_config.yaml \
- $ORIG/test/test_configs/star_override_1pass.yaml \
- --config sampletable=$ORIG/test/test_configs/two_samples.tsv \
- --until star
-
- echo "test PE reads"
- rm -r data && cp -r /tmp/data data
- ./run_test.sh -j 2 --use-conda -k -p -r --until multiqc \
- --configfile \
- $ORIG/test/test_configs/test_rnaseq_config.yaml \
- --config sampletable=$ORIG/test/test_configs/test_pe_sampletable.tsv
+ # Check the help for test/lcdb-wf-test to see what args these
+ # provide; some of them use the --until argument to restrict the
+ # rules that are run.
+ $DEPLOY/test/lcdb-wf-test rnaseq --run-workflow --sra-pe -k -r -p -j2 --use-conda
+ $DEPLOY/test/lcdb-wf-test rnaseq --run-workflow --sra-se -k -r -p -j2 --use-conda
+ $DEPLOY/test/lcdb-wf-test rnaseq --run-workflow --strandedness-pe -k -r -p -j2 --use-conda
+ $DEPLOY/test/lcdb-wf-test rnaseq --run-workflow --star-2pass -k -r -p -j2 --use-conda
+ $DEPLOY/test/lcdb-wf-test rnaseq --run-workflow --star-1pass -k -r -p -j2 --use-conda
+
# --------------------------------------------------------------------------
# Standard colocalization workflow
diff --git a/ci/ensure_docs.py b/ci/ensure_docs.py
old mode 100644
new mode 100755
index cee62f6d..232d8fab
--- a/ci/ensure_docs.py
+++ b/ci/ensure_docs.py
@@ -96,3 +96,7 @@ def get_headings(rst, underline="-"):
print("\n")
print("\n".join(errors))
sys.exit(1)
+
+else:
+ print("OK: found documentation for these identified chunks:")
+ print("- " + "\n- ".join(sorted(headings)))
diff --git a/test/lcdb-wf-test b/test/lcdb-wf-test
index 2c6e3633..3e04c7ba 100755
--- a/test/lcdb-wf-test
+++ b/test/lcdb-wf-test
@@ -3,168 +3,343 @@
"""
This script aims to make it more convenient to run various tests using
different configs.
+
+data: gets example data
+unit: runs unit tests (pytest, testthat, check urls, check docs)
+workflows: runs workflows and downstream tasks
+
+rnaseq:
+ standard:
+ desc: "Run main rnaseq workflow. Supply additional snakemake args."
+ command: "cd workflows/rnaseq && ./run_test.sh $SNAKEMAKE_ARGS"
+ trackhub:
+ desc: "Build the trackhub for rnaseq. Requires 'standard' to have been run"
+ command: "cd workflows/rnaseq && python rnaseq_trackhub.py config/config.yaml config/hub_config.yaml"
+
"""
import os
+import shlex
import subprocess as sp
import sys
from pathlib import Path
+import argparse
+import yaml
HERE = Path(__file__).resolve().parent
TOPLEVEL = Path(__file__).resolve().parent.parent
+WORKFLOW_ARGS = yaml.safe_load(open(TOPLEVEL / "test" / "workflow_test_params.yaml"))
+
-def get_data(kinds="all", branch="master", verbose=True):
+def print_header(name):
+ print("-" * 80)
+ print("lcdb-wf-test: ", name)
+ print("-" * 80)
+
+
+class Runner(object):
"""
- Download the test data from the lcdb-test-data repo
+ To add a new command, create a new method with a name starting with
+ "_cmd_", create a new ArgumentParser.
"""
- URL = "https://github.com/lcdb/lcdb-test-data/blob/{0}/data/{{}}?raw=true".format(
- branch
+
+ global_parser = argparse.ArgumentParser(add_help=False)
+ global_parser.add_argument(
+ "--env", default=str(TOPLEVEL / "env"), help="Main conda environment to use"
+ )
+ global_parser.add_argument(
+ "--env-r",
+ default=str(TOPLEVEL / "env-r"),
+ help="Conda environment containing R to use",
+ )
+ global_parser.add_argument(
+ "--orig",
+ default=str(TOPLEVEL),
+ help=f"""If specified, you can use the special string '__ORIG__' in
+ command line arguments (for example, when specifying config files).
+ Mostly used in CI.""",
)
- data_files = {
- "rnaseq": [
- (
- "rnaseq_samples/sample1/sample1.small_R1.fastq.gz",
- "workflows/rnaseq/data/example_data/rnaseq_sample1.fq.gz",
- ),
- (
- "rnaseq_samples/sample2/sample2.small_R1.fastq.gz",
- "workflows/rnaseq/data/example_data/rnaseq_sample2.fq.gz",
- ),
- (
- "rnaseq_samples/sample3/sample3.small_R1.fastq.gz",
- "workflows/rnaseq/data/example_data/rnaseq_sample3.fq.gz",
- ),
- (
- "rnaseq_samples/sample4/sample4.small_R1.fastq.gz",
- "workflows/rnaseq/data/example_data/rnaseq_sample4.fq.gz",
- ),
- (
- "rnaseq_samples/sample1/sample1.small_R1.fastq.gz",
- "workflows/rnaseq/data/example_data/rnaseq_sample1PE_1.fq.gz",
- ),
- (
- "rnaseq_samples/sample1/sample1.small_R2.fastq.gz",
- "workflows/rnaseq/data/example_data/rnaseq_sample1PE_2.fq.gz",
- ),
- (
- "rnaseq_samples/sample2/sample2.small_R1.fastq.gz",
- "workflows/rnaseq/data/example_data/rnaseq_sample2PE_1.fq.gz",
- ),
- (
- "rnaseq_samples/sample2/sample2.small_R2.fastq.gz",
- "workflows/rnaseq/data/example_data/rnaseq_sample2PE_2.fq.gz",
- ),
- ],
- "chipseq": [
- (
- "chipseq_samples/input_1/input_1.tiny_R1.fastq.gz",
- "workflows/chipseq/data/example_data/chipseq_input1.fq.gz",
- ),
- (
- "chipseq_samples/input_2/input_2.tiny_R1.fastq.gz",
- "workflows/chipseq/data/example_data/chipseq_input2.fq.gz",
- ),
- (
- "chipseq_samples/input_3/input_3.tiny_R1.fastq.gz",
- "workflows/chipseq/data/example_data/chipseq_input3.fq.gz",
- ),
- (
- "chipseq_samples/ip_1/ip_1.tiny_R1.fastq.gz",
- "workflows/chipseq/data/example_data/chipseq_ip1.fq.gz",
- ),
- (
- "chipseq_samples/ip_2/ip_2.tiny_R1.fastq.gz",
- "workflows/chipseq/data/example_data/chipseq_ip2.fq.gz",
- ),
- (
- "chipseq_samples/ip_3/ip_3.tiny_R1.fastq.gz",
- "workflows/chipseq/data/example_data/chipseq_ip3.fq.gz",
- ),
- (
- "chipseq_samples/ip_4/ip_4.tiny_R1.fastq.gz",
- "workflows/chipseq/data/example_data/chipseq_ip4.fq.gz",
- ),
- ],
- }
- cwd = os.getcwd()
- if str(cwd) != str(TOPLEVEL):
- raise ValueError(f"cwd: {cwd}; Please run this from the top level of the repo")
- if "all" in kinds:
- kinds = list(data_files.keys())
- for kind in kinds:
- for fn, dest in data_files[kind]:
- url = URL.format(fn)
- if verbose:
- print(f"downloading {url}")
- if dest is None:
- dest = fn
- dest = Path(dest)
- dest.parent.mkdir(parents=True, exist_ok=True)
- sp.run(f"wget -q -O- {url} > {dest}", shell=True, check=True)
-
-def run_pytest():
- sp.run(["pytest", "--doctest-modules", "lib"], check=True)
-
-def run_url_check():
- sys.path.insert(0, str(TOPLEVEL))
- from lib.common import check_all_urls_found
- check_all_urls_found()
-
-def r_package_check(env_r='./env-r'):
- sp.run([f"{env_r}/bin/Rscript", "-e", "testthat::test('lib/lcdbwf', export_all=TRUE)"])
-
-def snakefile(directory, args=None):
- sp.run(['bash', 'run_test.sh'] + args, cwd=TOPLEVEL / directory, check=True)
+ def __init__(self):
+ parser = argparse.ArgumentParser(
+ description="Test runner for lcdb-wf",
+ formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+ )
-if __name__ == "__main__":
+ choices = [i.replace("_cmd_", "") for i in dir(self) if i.startswith("_cmd_")]
- import argparse
+ parser.add_argument("command", help="Subcommand to run", choices=choices)
+ args = parser.parse_args(sys.argv[1:2])
+ if not hasattr(self, "_cmd_" + args.command):
+ print("Unrecognized command")
+ parser.print_help()
+ sys.exit(1)
+ getattr(self, "_cmd_" + args.command)()
- ap = argparse.ArgumentParser()
- ap.add_argument(
- "--get-data",
- action="store_true",
- help="Download example data. See --kinds argument for controlling this",
- )
- ap.add_argument(
- "--kinds",
- nargs="+",
- default="all",
- choices=["chipseq", "rnaseq", "all"],
- help="Download data for which workflows?"
- )
+ def _cmd_data(self):
+ parser = argparse.ArgumentParser(
+ description="Download data",
+ formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+ parents=[self.global_parser],
+ )
+
+ parser.add_argument(
+ "--kind",
+ default="all",
+ choices=["rnaseq", "chipseq"],
+ help="Kind of data to download",
+ )
+ parser.add_argument(
+ "--branch", default="main", help="Branch from lcdb-test-data to use"
+ )
+ parser.add_argument(
+ "--verbose",
+ action="store_true",
+ help="Be verbose about what's being downloaded",
+ )
+ args = parser.parse_args(sys.argv[2:])
- ap.add_argument('--env', default='./env', help="Specify main conda env. Default is %(default)s")
- ap.add_argument('--env-r', default='./env-r', help="Specify R conda env. Default is %(default)s")
- ap.add_argument('--pytest', action='store_true', help="Run pytest unit tests on lib directory")
- ap.add_argument('--urls', action='store_true', help='Check all URLs found across config files')
- ap.add_argument('--r-test', action='store_true', help='Run devtools::test on lcdbwf R package. Set R environment with --env-r.')
- ap.add_argument('--rnaseq', choices=['dryrun', 'standard'])
- ap.add_argument('--references', action='store_true')
- ap.add_argument('--cpus', help='Number of cores to use when calling snakemake, default is %(default)s', default='2')
- args = ap.parse_args()
- if args.get_data:
- get_data(kinds=args.kinds)
+ repo = "lcdb-test-data"
+ URL = f"https://github.com/lcdb/{repo}/blob/{args.branch}/data/{{}}?raw=true"
- if args.pytest:
- run_pytest()
+ # This dict maps files in the `data` directory of the repo to a local
+ # path to which it should be downloaded.
+ data_files = {
+ "rnaseq": [
+ (
+ "rnaseq_samples/sample1/sample1.small_R1.fastq.gz",
+ "workflows/rnaseq/data/example_data/rnaseq_sample1.fq.gz",
+ ),
+ (
+ "rnaseq_samples/sample2/sample2.small_R1.fastq.gz",
+ "workflows/rnaseq/data/example_data/rnaseq_sample2.fq.gz",
+ ),
+ (
+ "rnaseq_samples/sample3/sample3.small_R1.fastq.gz",
+ "workflows/rnaseq/data/example_data/rnaseq_sample3.fq.gz",
+ ),
+ (
+ "rnaseq_samples/sample4/sample4.small_R1.fastq.gz",
+ "workflows/rnaseq/data/example_data/rnaseq_sample4.fq.gz",
+ ),
+ (
+ "rnaseq_samples/sample1/sample1.small_R1.fastq.gz",
+ "workflows/rnaseq/data/example_data/rnaseq_sample1PE_1.fq.gz",
+ ),
+ (
+ "rnaseq_samples/sample1/sample1.small_R2.fastq.gz",
+ "workflows/rnaseq/data/example_data/rnaseq_sample1PE_2.fq.gz",
+ ),
+ (
+ "rnaseq_samples/sample2/sample2.small_R1.fastq.gz",
+ "workflows/rnaseq/data/example_data/rnaseq_sample2PE_1.fq.gz",
+ ),
+ (
+ "rnaseq_samples/sample2/sample2.small_R2.fastq.gz",
+ "workflows/rnaseq/data/example_data/rnaseq_sample2PE_2.fq.gz",
+ ),
+ ],
+ "chipseq": [
+ (
+ "chipseq_samples/input_1/input_1.tiny_R1.fastq.gz",
+ "workflows/chipseq/data/example_data/chipseq_input1.fq.gz",
+ ),
+ (
+ "chipseq_samples/input_2/input_2.tiny_R1.fastq.gz",
+ "workflows/chipseq/data/example_data/chipseq_input2.fq.gz",
+ ),
+ (
+ "chipseq_samples/input_3/input_3.tiny_R1.fastq.gz",
+ "workflows/chipseq/data/example_data/chipseq_input3.fq.gz",
+ ),
+ (
+ "chipseq_samples/ip_1/ip_1.tiny_R1.fastq.gz",
+ "workflows/chipseq/data/example_data/chipseq_ip1.fq.gz",
+ ),
+ (
+ "chipseq_samples/ip_2/ip_2.tiny_R1.fastq.gz",
+ "workflows/chipseq/data/example_data/chipseq_ip2.fq.gz",
+ ),
+ (
+ "chipseq_samples/ip_3/ip_3.tiny_R1.fastq.gz",
+ "workflows/chipseq/data/example_data/chipseq_ip3.fq.gz",
+ ),
+ (
+ "chipseq_samples/ip_4/ip_4.tiny_R1.fastq.gz",
+ "workflows/chipseq/data/example_data/chipseq_ip4.fq.gz",
+ ),
+ ],
+ }
- if args.urls:
- run_url_check()
+ if args.kind == "all":
+ kinds = list(data_files.keys())
+ else:
+ kinds = [args.kind]
+ for kind in kinds:
+ for fn, dest in data_files[kind]:
+ url = URL.format(fn)
+ if args.verbose:
+ print(f"downloading {url}")
+ if dest is None:
+ dest = fn
+ dest = Path(dest)
+ dest.parent.mkdir(parents=True, exist_ok=True)
+ sp.run(
+ f"wget -q -O- {url} > {dest}", shell=True, check=True, cwd=TOPLEVEL
+ )
- if args.r_test:
- r_package_check()
+ def _cmd_unit_tests(self):
+ parser = argparse.ArgumentParser(
+ description="Run various unit tests and checks",
+ parents=[self.global_parser],
+ formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+ )
+ parser.add_argument(
+ "--pytest",
+ action="store_true",
+ help="Run pytest unit tests and module doctests on lib/ directory",
+ )
+ parser.add_argument(
+ "--url-check",
+ action="store_true",
+ help="Ensure that URLs in config files (e.g., to genome references) are still valid",
+ )
+ parser.add_argument(
+ "--r-test",
+ action="store_true",
+ help="Run devtools::test on the lcdbwf R package. Be sure to check --env-r.",
+ )
- if args.rnaseq:
- if args.rnaseq == 'dryrun':
- snakefile('workflows/rnaseq', ['-n', '--use-conda'])
+ parser.add_argument(
+ "--ensure-docs",
+ action="store_true",
+ help="Ensure that all named R chunks are documented in the online help docs",
+ )
- if args.rnaseq == 'standard':
- snakefile('workflows/rnaseq', ['--use-conda', '-j', args.cpus, '-k', '-p', '-r'])
- sp.run(['python', 'rnaseq_trackhub.py', 'config/config.yaml', 'config/hub_config.yaml'], check=True, cwd='workflows/rnaseq')
+ args = parser.parse_args(sys.argv[2:])
+
+ if args.pytest:
+ print_header("pytest")
+ sp.run(["pytest", "--doctest-modules", "lib"], check=True, cwd=TOPLEVEL)
+
+ if args.url_check:
+ print_header("url check")
+ sys.path.insert(0, str(TOPLEVEL))
+ from lib.common import check_all_urls_found
+
+ check_all_urls_found()
+
+ if args.r_test:
+ sp.run(
+ [
+ f"{args.env_r}/bin/Rscript",
+ "-e",
+ "devtools::test('lib/lcdbwf', export_all=TRUE)",
+ ]
+ )
+
+ if args.ensure_docs:
+ sp.run(["./ensure_docs.py"], check=True, cwd=TOPLEVEL / "ci")
+
+ def _cmd_rnaseq(self):
+ parser = argparse.ArgumentParser(
+ description="Run rnaseq workflow and downstream tests",
+ parents=[self.global_parser],
+ formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+ )
+ parser.add_argument(
+ "--run-workflow",
+ action="store_true",
+ help="""Run rnaseq workflow using the run_tesh.sh harness, which
+ edits the Snakefile to use test settings before running. Additional
+ args not specified here are passed to Snakemake, or use other flags
+ below to easily specify config sets.""",
+ )
+ parser.add_argument(
+ "--trackhub", action="store_true", help="Build the rnaseq track hub"
+ )
+ parser.add_argument(
+ "--downstream",
+ action="store_true",
+ help="""Run the downstream rnaseq.Rmd, via
+ workflows/rnaseq/run_downstream_test.sh. This runs the preprocessor
+ on the files to allow the use of # [TEST SETTINGS] comments; see
+ that script for detail.s Make sure --env-r is set correctly""",
+ )
+ group = parser.add_mutually_exclusive_group()
+ workflow_prefix = "bash run_test.sh"
+ workflow_dir = "workflow/rnaseq"
+ for key, val in WORKFLOW_ARGS["rnaseq"].items():
+ group.add_argument(
+ "--" + key,
+ action="store_const",
+ default="",
+ dest="additional_args",
+ const=val["args"],
+ help=f"""GROUP: Part of mutually exclusive rnaseq group. Runs the
+ following: cd {workflow_dir} && {workflow_prefix}
+ {val['args']}. See workflow_test_params.yaml for details.""",
+ )
+
+ args, extra = parser.parse_known_args(sys.argv[2:])
+
+ if args.run_workflow:
+ print(args)
+ if args.additional_args:
+ extra.extend(shlex.split(args.additional_args))
+
+ extra = [i.replace("__ORIG__", args.orig) for i in extra]
+ strargs = " ".join(extra)
+ print_header(f"Running workflows/rnaseq/run_test.sh with args: {strargs}")
+ sp.run(
+ shlex.split(workflow_prefix) + extra,
+ cwd=TOPLEVEL / "workflows/rnaseq",
+ check=True,
+ )
+ if args.trackhub:
+ print_header("running trackhub script")
+ sp.run(
+ [
+ "python",
+ "rnaseq_trackhub.py",
+ "config/config.yaml",
+ "config/hub_config.yaml",
+ ],
+ check=True,
+ cwd="workflows/rnaseq",
+ )
+ print("See workflows/rnaseq/staging for the built trackhub")
+
+ if args.downstream:
+ print_header("running downstream rnaseq.Rmd")
+ sp.run(
+ [
+ "bash",
+ "run_downstream_test.sh",
+ ],
+ env={"ENV_R": args.env_r, **os.environ},
+ cwd="workflows/rnaseq",
+ )
+
+
+if __name__ == "__main__":
+ Runner()
+if __name__ == "__mn__":
if args.references:
- snakefile('workflows/references', ['--use-conda', '-j', args.cpus, '-k', '-p', '-r', '--configfile', 'config/config.yaml'])
+ print_header("references")
+ snakefile(
+ "workflows/references",
+ snakemake_args=[
+ "--use-conda",
+ "-j",
+ args.cpus,
+ "-k",
+ "-p",
+ "-r",
+ "--configfile",
+ "config/config.yaml",
+ ],
+ )
# vim: ft=python
diff --git a/test/test_configs/star_1pass.tsv b/test/test_configs/star_1pass.tsv
new file mode 100644
index 00000000..3c73275e
--- /dev/null
+++ b/test/test_configs/star_1pass.tsv
@@ -0,0 +1,3 @@
+samplename group layout orig_filename
+sample1-star-1pass control SE data/example_data/rnaseq_sample1PE_1.fq.gz
+sample2-star-1pass control SE data/example_data/rnaseq_sample2.fq.gz
diff --git a/test/test_configs/star_2pass.tsv b/test/test_configs/star_2pass.tsv
new file mode 100644
index 00000000..8cf98eb0
--- /dev/null
+++ b/test/test_configs/star_2pass.tsv
@@ -0,0 +1,3 @@
+samplename group layout orig_filename
+sample1-star-2pass control SE data/example_data/rnaseq_sample1PE_1.fq.gz
+sample2-star-2pass control SE data/example_data/rnaseq_sample2.fq.gz
diff --git a/test/test_configs/test_sra_sampletable_SE_only.tsv b/test/test_configs/test_sra_sampletable_SE_only.tsv
index 486e9396..6b403643 100644
--- a/test/test_configs/test_sra_sampletable_SE_only.tsv
+++ b/test/test_configs/test_sra_sampletable_SE_only.tsv
@@ -1,4 +1,4 @@
samplename Run layout
-sra1 SRR948304 SINGLE
-sra2 SRR948304 SINGLE
-sra3 SRR948305 SINGLE
+sra4 SRR948304 SINGLE
+sra5 SRR948304 SINGLE
+sra6 SRR948305 SINGLE
diff --git a/test/test_configs/two_samples.tsv b/test/test_configs/two_samples.tsv
index 30886104..57ccb7d9 100644
--- a/test/test_configs/two_samples.tsv
+++ b/test/test_configs/two_samples.tsv
@@ -1,3 +1,3 @@
samplename group layout orig_filename
-sample1 control SE data/example_data/rnaseq_sample1PE_1.fq.gz
-sample2 control SE data/example_data/rnaseq_sample2.fq.gz
+sample1_of_2 control SE data/example_data/rnaseq_sample1PE_1.fq.gz
+sample2_of_2 control SE data/example_data/rnaseq_sample2.fq.gz
diff --git a/test/workflow_test_params.yaml b/test/workflow_test_params.yaml
new file mode 100644
index 00000000..f396f9d3
--- /dev/null
+++ b/test/workflow_test_params.yaml
@@ -0,0 +1,61 @@
+# NOTE:
+#
+# The "__ORIG__" placeholder is a mechanism for allowing the CI to run config
+# files from a full cloned repo within a deployed directory. The __ORIG__ will
+# be filled in with the lcdb-wf-test "--orig" argument, which defaults to the
+# top-level repo dir.
+#
+# In other words, "__ORIG__/" will be replaced with the top-level dir unless
+# you specify --orig.
+#
+#
+# NOTE:
+# These arguments are pulled into the test/lcdb-wf-test runner script
+# automatically.
+
+rnaseq:
+ sra-pe:
+ args: |
+ --until cutadapt
+ --configfile __ORIG__/test/test_configs/test_rnaseq_config.yaml
+ --config sampletable=__ORIG__/test/test_configs/test_sra_sampletable.tsv
+
+ sra-se:
+ args: |
+ --until cutadapt
+ --configfile __ORIG__/test/test_configs/test_rnaseq_config.yaml
+ --config sampletable=__ORIG__/test/test_configs/test_sra_sampletable_SE_only.tsv
+
+ strandedness-pe:
+ args: |
+ --until strand_check
+ --configfile __ORIG__/test/test_configs/test_rnaseq_config.yaml
+ --config sampletable=__ORIG__/test/test_configs/test_pe_sampletable.tsv
+
+ strandedness-se:
+ args: |
+ --until strand_check
+ --configfile __ORIG__/test/test_configs/test_rnaseq_config.yaml
+ --config sampletable=__ORIG__/test/test_configs/two_samples.tsv
+
+ star-2pass:
+ args: |
+ --until star_pass2
+ --configfile
+ __ORIG__/test/test_configs/test_rnaseq_config.yaml
+ __ORIG__/test/test_configs/star_override_2pass.yaml
+ --config sampletable=__ORIG__/test/test_configs/star_2pass.tsv
+
+ star-1pass:
+ args: |
+ --until star
+ --configfile
+ __ORIG__/test/test_configs/test_rnaseq_config.yaml
+ __ORIG__/test/test_configs/star_override_1pass.yaml
+ --config sampletable=__ORIG__/test/test_configs/star_1pass.tsv
+
+pe:
+ args: |
+ --until multiqc
+ --configfile __ORIG__/test/test_configs/test_rnaseq_config.yaml
+ --config sampletable=__ORIG__/test/test_configs/test_pe_sampletable.tsv
diff --git a/workflows/rnaseq/run_downstream_test.sh b/workflows/rnaseq/run_downstream_test.sh
index 6440d5a1..57ad932d 100755
--- a/workflows/rnaseq/run_downstream_test.sh
+++ b/workflows/rnaseq/run_downstream_test.sh
@@ -19,4 +19,12 @@ done
cp downstream/config.yaml downstream-test/config.yaml
cp downstream/text.yaml downstream-test/text.yaml
+if [ -z "$ENV_R" ]; then
+ echo Please set \$ENV_R to the conda env containing R and retry. Exiting.
+ exit 1
+fi
+
+eval "$(conda shell.bash hook)"
+conda activate $ENV_R
Rscript -e "rmarkdown::render('downstream-test/rnaseq.Rmd')"
+conda deactivate
From 6f90e6739492f5cfde324504cac4661ce37c7da9 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Tue, 22 Nov 2022 20:51:47 -0500
Subject: [PATCH 25/91] fix ci config typo
---
.circleci/config.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index b1a63dc1..f2b02c6d 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -211,7 +211,7 @@ variables:
# This run the preprocessor on the Rmd files and stores them
# in a new download-test directory (see the comments in the script
# for details)
- $DEPLOY/ test/lcdb-wf-test rnaseq --downstream
+ $DEPLOY/test/lcdb-wf-test rnaseq --downstream
# bundle up the entire directory to be used as an artifact
tar -zcf downstream.tar.gz downstream-test/
From ece7c1a62aa8108b4082c802a92dacb2dfc13956 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Tue, 22 Nov 2022 21:00:29 -0500
Subject: [PATCH 26/91] remove redundant libsizes rules
addresses #342
---
workflows/chipseq/Snakefile | 56 -------------------------------------
workflows/rnaseq/Snakefile | 56 -------------------------------------
2 files changed, 112 deletions(-)
diff --git a/workflows/chipseq/Snakefile b/workflows/chipseq/Snakefile
index 401448c6..532bceae 100644
--- a/workflows/chipseq/Snakefile
+++ b/workflows/chipseq/Snakefile
@@ -59,9 +59,7 @@ def wrapper_for(path):
final_targets = utils.flatten((
c.targets['bam'],
utils.flatten(c.targets['fastqc']),
- utils.flatten(c.targets['libsizes']),
[c.targets['fastq_screen']],
- [c.targets['libsizes_table']],
[c.targets['multiqc']],
utils.flatten(c.targets['markduplicates']),
utils.flatten(c.targets['bigwig']),
@@ -320,62 +318,8 @@ rule fastq_screen:
wrapper_for('fastq_screen/wrapper.py')
-rule libsizes_table:
- """
- Aggregate fastq and bam counts in to a single table
- """
- input:
- utils.flatten(c.targets['libsizes'])
- output:
- json=c.patterns['libsizes_yaml'],
- tsv=c.patterns['libsizes_table']
- run:
- def sample(f):
- return os.path.basename(os.path.dirname(f))
-
- def million(f):
- return float(open(f).read()) / 1e6
-
- def stage(f):
- return os.path.basename(f).split('.', 1)[1].replace('.gz', '').replace('.count', '')
-
- df = pd.DataFrame(dict(filename=list(map(str, input))))
- df['sample'] = df.filename.apply(sample)
- df['million'] = df.filename.apply(million)
- df['stage'] = df.filename.apply(stage)
- df = df.set_index('filename')
- df = df.pivot('sample', columns='stage', values='million')
-
- # make nicer column names
- convert = {
- 'fastq.libsize': 'stage1_raw',
- 'cutadapt.fastq.libsize' : 'stage2_trimmed',
- 'cutadapt.bam.libsize': 'stage3_aligned',
- 'cutadapt.unique.bam.libsize': 'stage4_unique',
- 'cutadapt.unique.nodups.bam.libsize': 'stage5_nodups',
- }
-
- df.columns = [convert[i] for i in df.columns]
-
- df.to_csv(output.tsv, sep='\t')
- y = {
- 'id': 'libsizes_table',
- 'section_name': 'Library sizes',
- 'description': 'Library sizes at various stages of the pipeline',
- 'plot_type': 'table',
- 'pconfig': {
- 'id': 'libsizes_table_table',
- 'title': 'Library size table',
- 'min': 0
- },
- 'data': yaml.load(df.transpose().to_json(), Loader=yaml.FullLoader),
- }
- with open(output.json, 'w') as fout:
- yaml.dump(y, fout, default_flow_style=False)
-
multiqc_inputs = [
utils.flatten(c.targets['fastqc']) +
- utils.flatten(c.targets['libsizes_yaml']) +
utils.flatten(c.targets['cutadapt']) +
utils.flatten(c.targets['bam']) +
utils.flatten(c.targets['markduplicates']) +
diff --git a/workflows/rnaseq/Snakefile b/workflows/rnaseq/Snakefile
index e086402d..a41b28e9 100644
--- a/workflows/rnaseq/Snakefile
+++ b/workflows/rnaseq/Snakefile
@@ -51,9 +51,7 @@ def wrapper_for(path):
# See "patterns and targets" in the documentation for what's going on here.
final_targets = utils.flatten((
utils.flatten(c.targets['fastqc']),
- utils.flatten(c.targets['libsizes']),
[c.targets['fastq_screen']],
- [c.targets['libsizes_table']],
[c.targets['rrna_percentages_table']],
[c.targets['multiqc']],
utils.flatten(c.targets['featurecounts']),
@@ -625,59 +623,6 @@ rule rrna_libsizes_table:
yaml.dump(y, fout, default_flow_style=False)
-rule libsizes_table:
- """
- Aggregate fastq and bam counts in to a single table
- """
- input:
- utils.flatten(c.targets['libsizes'])
- output:
- json=c.patterns['libsizes_yaml'],
- tsv=c.patterns['libsizes_table']
- run:
- def sample(f):
- return os.path.basename(os.path.dirname(f))
-
- def million(f):
- return float(open(f).read()) / 1e6
-
- def stage(f):
- return os.path.basename(f).split('.', 1)[1].replace('.gz', '').replace('.count', '')
-
- df = pd.DataFrame(dict(filename=list(map(str, input))))
- df['sample'] = df.filename.apply(sample)
- df['million'] = df.filename.apply(million)
- df['stage'] = df.filename.apply(stage)
- df = df.set_index('filename')
- df = df.pivot('sample', columns='stage', values='million')
-
- # make nicer column names
- convert = {
- 'fastq.libsize': 'stage1_raw',
- 'cutadapt.fastq.libsize' : 'stage2_trimmed',
- 'cutadapt.bam.libsize': 'stage3_aligned',
- }
-
- df.columns = [convert[i] for i in df.columns]
-
- df.to_csv(output.tsv, sep='\t')
- y = {
- 'id': 'libsizes_table',
- 'section_name': 'Library sizes',
- 'description': 'Library sizes at various stages of the pipeline',
- 'plot_type': 'table',
- 'pconfig': {
- 'id': 'libsizes_table_table',
- 'title': 'Library size table',
- 'min': 0
- },
- 'data': yaml.load(df.transpose().to_json(), Loader=yaml.FullLoader),
- }
- with open(output.json, 'w') as fout:
- yaml.dump(y, fout, default_flow_style=False)
-
-
-
rule multiqc:
"""
Aggregate various QC stats and logs into a single HTML report with MultiQC
@@ -687,7 +632,6 @@ rule multiqc:
input:
files=(
utils.flatten(c.targets['fastqc']) +
- utils.flatten(c.targets['libsizes_yaml']) +
utils.flatten(c.targets['rrna_percentages_yaml']) +
utils.flatten(c.targets['cutadapt']) +
utils.flatten(c.targets['featurecounts']) +
From 33f2948d0fb3ad44e09b9ad7d8325bb62535831e Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Wed, 23 Nov 2022 10:14:19 -0500
Subject: [PATCH 27/91] default to correct branch
---
test/lcdb-wf-test | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/test/lcdb-wf-test b/test/lcdb-wf-test
index 3e04c7ba..188cd502 100755
--- a/test/lcdb-wf-test
+++ b/test/lcdb-wf-test
@@ -90,7 +90,7 @@ class Runner(object):
help="Kind of data to download",
)
parser.add_argument(
- "--branch", default="main", help="Branch from lcdb-test-data to use"
+ "--branch", default="master", help="Branch from lcdb-test-data to use"
)
parser.add_argument(
"--verbose",
From fd56a35e4689a85db2a7fe7a0afe3be7e723f78e Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Wed, 23 Nov 2022 10:15:07 -0500
Subject: [PATCH 28/91] improve docs and help for testing script
---
test/lcdb-wf-test | 12 +++++++++---
test/workflow_test_params.yaml | 26 ++++++++++++++++----------
2 files changed, 25 insertions(+), 13 deletions(-)
diff --git a/test/lcdb-wf-test b/test/lcdb-wf-test
index 188cd502..38c59b7b 100755
--- a/test/lcdb-wf-test
+++ b/test/lcdb-wf-test
@@ -203,12 +203,13 @@ class Runner(object):
parser.add_argument(
"--url-check",
action="store_true",
- help="Ensure that URLs in config files (e.g., to genome references) are still valid",
+ help="Ensure that URLs found in config files (e.g., to genome references) are still valid",
)
parser.add_argument(
"--r-test",
action="store_true",
- help="Run devtools::test on the lcdbwf R package. Be sure to check --env-r.",
+ help="""Run devtools::test on the lcdbwf R package. Activates the
+ conda environment specified by --env-r just before running.""",
)
parser.add_argument(
@@ -243,6 +244,10 @@ class Runner(object):
sp.run(["./ensure_docs.py"], check=True, cwd=TOPLEVEL / "ci")
def _cmd_rnaseq(self):
+ """
+ This function handles the "rnaseq" subcommand.
+ """
+
parser = argparse.ArgumentParser(
description="Run rnaseq workflow and downstream tests",
parents=[self.global_parser],
@@ -267,6 +272,7 @@ class Runner(object):
on the files to allow the use of # [TEST SETTINGS] comments; see
that script for detail.s Make sure --env-r is set correctly""",
)
+
group = parser.add_mutually_exclusive_group()
workflow_prefix = "bash run_test.sh"
workflow_dir = "workflow/rnaseq"
@@ -279,7 +285,7 @@ class Runner(object):
const=val["args"],
help=f"""GROUP: Part of mutually exclusive rnaseq group. Runs the
following: cd {workflow_dir} && {workflow_prefix}
- {val['args']}. See workflow_test_params.yaml for details.""",
+ {val['args']}. {val['desc']} Configured in workflow_test_params.yaml.""",
)
args, extra = parser.parse_known_args(sys.argv[2:])
diff --git a/test/workflow_test_params.yaml b/test/workflow_test_params.yaml
index f396f9d3..f04cfe40 100644
--- a/test/workflow_test_params.yaml
+++ b/test/workflow_test_params.yaml
@@ -1,44 +1,48 @@
+# This file configures arguments for running various workflows that are pulled
+# into the test/lcdb-wf-test runner script automatically. It is a way of
+#
# NOTE:
#
# The "__ORIG__" placeholder is a mechanism for allowing the CI to run config
-# files from a full cloned repo within a deployed directory. The __ORIG__ will
-# be filled in with the lcdb-wf-test "--orig" argument, which defaults to the
-# top-level repo dir.
-#
-# In other words, "__ORIG__/" will be replaced with the top-level dir unless
-# you specify --orig.
+# files living in a full cloned repo, but within a (different) deployed
+# directory. The __ORIG__ indicates the full cloned repo and will be filled in
+# with the lcdb-wf-test "--orig" argument, which defaults to the top-level repo
+# dir.
#
-#
-# NOTE:
-# These arguments are pulled into the test/lcdb-wf-test runner script
-# automatically.
+# For local testing, don't specify --orig and leave the default. This will
+# automatically fill in the top-level dir of the current repo.
rnaseq:
sra-pe:
+ desc: Tests paired-end data downloaded directly from SRA. Only run until the cutadapt rule.
args: |
--until cutadapt
--configfile __ORIG__/test/test_configs/test_rnaseq_config.yaml
--config sampletable=__ORIG__/test/test_configs/test_sra_sampletable.tsv
sra-se:
+ desc: Tests single-end data downloaded directly from SRA. Only run until the cutadapt rule.
args: |
--until cutadapt
--configfile __ORIG__/test/test_configs/test_rnaseq_config.yaml
--config sampletable=__ORIG__/test/test_configs/test_sra_sampletable_SE_only.tsv
strandedness-pe:
+ desc: Tests running the strandedness pre-check using paired-end data.
args: |
--until strand_check
--configfile __ORIG__/test/test_configs/test_rnaseq_config.yaml
--config sampletable=__ORIG__/test/test_configs/test_pe_sampletable.tsv
strandedness-se:
+ desc: Tests running the strandedness pre-check using single-ended data.
args: |
--until strand_check
--configfile __ORIG__/test/test_configs/test_rnaseq_config.yaml
--config sampletable=__ORIG__/test/test_configs/two_samples.tsv
star-2pass:
+ desc: Tests running STAR in 2-pass mode. Only runs until the star_pass2 rule.
args: |
--until star_pass2
--configfile
@@ -47,6 +51,7 @@ rnaseq:
--config sampletable=__ORIG__/test/test_configs/star_2pass.tsv
star-1pass:
+ desc: Tests running STAR in 1-pass (default) mode. Only runs until the star rule.
args: |
--until star
--configfile
@@ -55,6 +60,7 @@ rnaseq:
--config sampletable=__ORIG__/test/test_configs/star_1pass.tsv
pe:
+ desc: Tests paired-end data
args: |
--until multiqc
--configfile __ORIG__/test/test_configs/test_rnaseq_config.yaml
From c6765a16e63cb98cfb1d33480c785e706b27b33c Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Wed, 23 Nov 2022 10:15:24 -0500
Subject: [PATCH 29/91] ensure configured env-r is activated before testing lib
---
test/lcdb-wf-test | 12 +++++++-----
1 file changed, 7 insertions(+), 5 deletions(-)
diff --git a/test/lcdb-wf-test b/test/lcdb-wf-test
index 38c59b7b..2a96dd7b 100755
--- a/test/lcdb-wf-test
+++ b/test/lcdb-wf-test
@@ -232,12 +232,14 @@ class Runner(object):
check_all_urls_found()
if args.r_test:
+ print_header("R test")
sp.run(
- [
- f"{args.env_r}/bin/Rscript",
- "-e",
- "devtools::test('lib/lcdbwf', export_all=TRUE)",
- ]
+ 'eval "$(conda shell.bash hook)" '
+ f"&& conda activate {args.env_r} "
+ '''&& Rscript -e "devtools::test('lib/lcdbwf', export_all=TRUE)"''',
+ shell=True,
+ check=True,
+ executable="/bin/bash"
)
if args.ensure_docs:
From 0abaa4604e87010f415ef1af421d5c06bbb7faaf Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Wed, 23 Nov 2022 20:55:46 -0500
Subject: [PATCH 30/91] improvements to testing config and script
---
.circleci/config.yml | 27 ++++++++------
test/lcdb-wf-test | 47 +++++++++++++++----------
workflows/rnaseq/run_downstream_test.sh | 8 -----
3 files changed, 44 insertions(+), 38 deletions(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index f2b02c6d..b43f5828 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -50,6 +50,8 @@ variables:
# x11-utils required to avoid R::png() segfaulting
apt update && apt install -y locales-all locales x11-utils
echo 'export DEPLOY=/tmp/lcdb-wf-test' >> $BASH_ENV
+ echo 'export LCDBWF_ENV=lcdb-wf-test' >> $BASH_ENV
+ echo 'export LCDBWF_ENV_R=lcdb-wf-test-r' >> $BASH_ENV
echo 'export LC_ALL=en_US.utf8' >> $BASH_ENV
echo 'export LANG=en_US.utf8' >> $BASH_ENV
source $BASH_ENV
@@ -72,8 +74,8 @@ variables:
conda config --system --add channels bioconda
conda config --system --add channels conda-forge
conda install mamba -y
- mamba env create -n lcdb-wf-test --file env.yml
- mamba env create -n lcdb-wf-test-r --file env-r.yml
+ mamba env create -n $LCDBWF_ENV --file env.yml
+ mamba env create -n $LCDBWF_ENV_R --file env-r.yml
fi
# --------------------------------------------------------------------------
@@ -127,7 +129,7 @@ variables:
test/lcdb-wf-test unit_tests --url-check
# run R package unit tests using the R env
- test/lcdb-wf-test unit_tests --r-test --env-r lcdb-wf-test-r
+ test/lcdb-wf-test unit_tests --r-test
# --------------------------------------------------------------------------
@@ -199,9 +201,9 @@ variables:
command: |
cd $DEPLOY
source activate lcdb-wf-test
- $DEPLOY/test/lcdb-wf-test rnaseq --run-workflow --use-conda -j2 -k -p -r
+ $DEPLOY/test/lcdb-wf-test rnaseq --run-workflow --use-conda -j2 -k -p -r --orig $ORIG
- $DEPLOY/test/lcdb-wf-test rnaseq --trackhub
+ $DEPLOY/test/lcdb-wf-test rnaseq --trackhub --orig $ORIG
# Starting in v1.6, we separate out the non-R from the
# R environments. So we need to test the rnaseq.Rmd separately
@@ -229,12 +231,15 @@ variables:
# Check the help for test/lcdb-wf-test to see what args these
# provide; some of them use the --until argument to restrict the
- # rules that are run.
- $DEPLOY/test/lcdb-wf-test rnaseq --run-workflow --sra-pe -k -r -p -j2 --use-conda
- $DEPLOY/test/lcdb-wf-test rnaseq --run-workflow --sra-se -k -r -p -j2 --use-conda
- $DEPLOY/test/lcdb-wf-test rnaseq --run-workflow --strandedness-pe -k -r -p -j2 --use-conda
- $DEPLOY/test/lcdb-wf-test rnaseq --run-workflow --star-2pass -k -r -p -j2 --use-conda
- $DEPLOY/test/lcdb-wf-test rnaseq --run-workflow --star-1pass -k -r -p -j2 --use-conda
+ # rules that are run. Note the use of --orig $ORIG to use the test
+ # configs from the original clone rather than the deployed directory.
+ $DEPLOY/test/lcdb-wf-test rnaseq --run-workflow --sra-pe -k -r -p -j2 --use-conda --orig $ORIG
+ $DEPLOY/test/lcdb-wf-test rnaseq --run-workflow --sra-se -k -r -p -j2 --use-conda --orig $ORIG
+ $DEPLOY/test/lcdb-wf-test rnaseq --run-workflow --strandedness-pe -k -r -p -j2 --use-conda --orig $ORIG
+ $DEPLOY/test/lcdb-wf-test rnaseq --run-workflow --star-2pass -k -r -p -j2 --use-conda --orig $ORIG
+ $DEPLOY/test/lcdb-wf-test rnaseq --run-workflow --star-1pass -k -r -p -j2 --use-conda --orig $ORIG
+ $DEPLOY/test/lcdb-wf-test rnaseq --run-workflow --pe -k -r -p -j2 --use-conda --orig $ORIG
+
# --------------------------------------------------------------------------
diff --git a/test/lcdb-wf-test b/test/lcdb-wf-test
index 2a96dd7b..fb7adf39 100755
--- a/test/lcdb-wf-test
+++ b/test/lcdb-wf-test
@@ -43,27 +43,32 @@ class Runner(object):
"_cmd_", create a new ArgumentParser.
"""
+ default_env = os.getenv("LCDBWF_ENV", str(TOPLEVEL / "env"))
+ default_env_r = os.getenv("LCDBWF_ENV_R", str(TOPLEVEL / "env-r"))
global_parser = argparse.ArgumentParser(add_help=False)
global_parser.add_argument(
- "--env", default=str(TOPLEVEL / "env"), help="Main conda environment to use"
+ "--env", default=default_env,
+ help=f"""Main conda environment to use. Override
+ by setting $LCDBWF_ENV or override that by explicity setting --env. Currently will use {default_env}"""
)
global_parser.add_argument(
"--env-r",
- default=str(TOPLEVEL / "env-r"),
- help="Conda environment containing R to use",
+ default=default_env_r,
+ help=f"""Main R conda environment to use. Override by setting
+ $LCDBWF_ENV_R or override that by explicity setting --env-r. Currently
+ will use {default_env_r}"""
)
global_parser.add_argument(
"--orig",
default=str(TOPLEVEL),
help=f"""If specified, you can use the special string '__ORIG__' in
- command line arguments (for example, when specifying config files).
- Mostly used in CI.""",
+ command line arguments which will be filled in with the value provided
+ here. Mostly used in CI.""",
)
def __init__(self):
parser = argparse.ArgumentParser(
description="Test runner for lcdb-wf",
- formatter_class=argparse.ArgumentDefaultsHelpFormatter,
)
choices = [i.replace("_cmd_", "") for i in dir(self) if i.startswith("_cmd_")]
@@ -79,7 +84,6 @@ class Runner(object):
def _cmd_data(self):
parser = argparse.ArgumentParser(
description="Download data",
- formatter_class=argparse.ArgumentDefaultsHelpFormatter,
parents=[self.global_parser],
)
@@ -193,7 +197,6 @@ class Runner(object):
parser = argparse.ArgumentParser(
description="Run various unit tests and checks",
parents=[self.global_parser],
- formatter_class=argparse.ArgumentDefaultsHelpFormatter,
)
parser.add_argument(
"--pytest",
@@ -253,7 +256,6 @@ class Runner(object):
parser = argparse.ArgumentParser(
description="Run rnaseq workflow and downstream tests",
parents=[self.global_parser],
- formatter_class=argparse.ArgumentDefaultsHelpFormatter,
)
parser.add_argument(
"--run-workflow",
@@ -272,9 +274,15 @@ class Runner(object):
help="""Run the downstream rnaseq.Rmd, via
workflows/rnaseq/run_downstream_test.sh. This runs the preprocessor
on the files to allow the use of # [TEST SETTINGS] comments; see
- that script for detail.s Make sure --env-r is set correctly""",
+ that script for details. Activates environment configured in
+ --env-r before running.""",
)
+ # Here we programmatically build the parser from the
+ # workflow_test_params.yaml file. They are added to
+ # a mutually-exclusive group to avoid overwriting each others' config
+ # file params. They all write their params to the args.additional_args
+ # attribute.
group = parser.add_mutually_exclusive_group()
workflow_prefix = "bash run_test.sh"
workflow_dir = "workflow/rnaseq"
@@ -285,9 +293,10 @@ class Runner(object):
default="",
dest="additional_args",
const=val["args"],
- help=f"""GROUP: Part of mutually exclusive rnaseq group. Runs the
- following: cd {workflow_dir} && {workflow_prefix}
- {val['args']}. {val['desc']} Configured in workflow_test_params.yaml.""",
+ help=f"""GROUP: Part of mutually exclusive rnaseq group. Runs
+ the following: cd {workflow_dir} && {workflow_prefix}
+ {val['args']}. {val['desc']} Configured in
+ workflow_test_params.yaml.""",
)
args, extra = parser.parse_known_args(sys.argv[2:])
@@ -322,12 +331,12 @@ class Runner(object):
if args.downstream:
print_header("running downstream rnaseq.Rmd")
sp.run(
- [
- "bash",
- "run_downstream_test.sh",
- ],
- env={"ENV_R": args.env_r, **os.environ},
- cwd="workflows/rnaseq",
+ 'eval "$(conda shell.bash hook)" '
+ f"&& conda activate {args.env_r} "
+ "&& (cd workflows/rnaseq && bash run_downstream_test.sh)",
+ shell=True,
+ check=True,
+ executable="/bin/bash"
)
diff --git a/workflows/rnaseq/run_downstream_test.sh b/workflows/rnaseq/run_downstream_test.sh
index 57ad932d..ba0fa79b 100755
--- a/workflows/rnaseq/run_downstream_test.sh
+++ b/workflows/rnaseq/run_downstream_test.sh
@@ -18,13 +18,5 @@ done
# Make sure we move the config file there too
cp downstream/config.yaml downstream-test/config.yaml
cp downstream/text.yaml downstream-test/text.yaml
-
-if [ -z "$ENV_R" ]; then
- echo Please set \$ENV_R to the conda env containing R and retry. Exiting.
- exit 1
-fi
-
-eval "$(conda shell.bash hook)"
-conda activate $ENV_R
Rscript -e "rmarkdown::render('downstream-test/rnaseq.Rmd')"
conda deactivate
From 6a5413bfc9753e8a7f528e354bc2c4604d563990 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Wed, 23 Nov 2022 21:13:19 -0500
Subject: [PATCH 31/91] minor tweaks to r tests
---
lib/lcdbwf/R/loading.R | 3 +++
workflows/rnaseq/run_downstream_test.sh | 1 -
2 files changed, 3 insertions(+), 1 deletion(-)
diff --git a/lib/lcdbwf/R/loading.R b/lib/lcdbwf/R/loading.R
index 9ff0eae1..68fcc818 100644
--- a/lib/lcdbwf/R/loading.R
+++ b/lib/lcdbwf/R/loading.R
@@ -22,6 +22,9 @@ DESeqDataSetFromCombinedFeatureCounts <- function(filename, sampletable,
sample_func=lcdbwf_samplename,
subset_counts=FALSE, ...){
+ if (is.null(subset_counts)){
+ subset_counts <- FALSE
+ }
# The sampletable may be data.frame or tibble; if it's a tibble then it
# likely doesn't have rownames. So in this function we assume that it's the
# first column that contains the samplenames.
diff --git a/workflows/rnaseq/run_downstream_test.sh b/workflows/rnaseq/run_downstream_test.sh
index ba0fa79b..7544c5dd 100755
--- a/workflows/rnaseq/run_downstream_test.sh
+++ b/workflows/rnaseq/run_downstream_test.sh
@@ -19,4 +19,3 @@ done
cp downstream/config.yaml downstream-test/config.yaml
cp downstream/text.yaml downstream-test/text.yaml
Rscript -e "rmarkdown::render('downstream-test/rnaseq.Rmd')"
-conda deactivate
From b088449135da4e7e02ec81d9be975066e5f70e75 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Wed, 23 Nov 2022 21:21:38 -0500
Subject: [PATCH 32/91] minor test fixes
---
.circleci/config.yml | 9 ++++-----
test/lcdb-wf-test | 13 -------------
2 files changed, 4 insertions(+), 18 deletions(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index b43f5828..e3ba5d12 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -48,7 +48,7 @@ variables:
name: Set path
command: |
# x11-utils required to avoid R::png() segfaulting
- apt update && apt install -y locales-all locales x11-utils
+ apt update && apt install -y locales-all locales rsync x11-utils
echo 'export DEPLOY=/tmp/lcdb-wf-test' >> $BASH_ENV
echo 'export LCDBWF_ENV=lcdb-wf-test' >> $BASH_ENV
echo 'export LCDBWF_ENV_R=lcdb-wf-test-r' >> $BASH_ENV
@@ -62,10 +62,6 @@ variables:
name: Setup conda
command: |
set -e
- apt update
- apt install -y locales-all locales
- export LC_ALL=en_US.utf8
- export LANG=en_US.utf8
# We only do the installation if the conda environment does not already
# exist.
if ! conda env list | grep -q "lcdb-wf-test"; then
@@ -119,6 +115,9 @@ variables:
command: |
source activate lcdb-wf-test
+ echo LCDBWF_ENV_R=$LCDBWF_ENV_R
+ echo LCDBWF_ENV=$LCDBWF_ENV
+
# run unit tests and doctests for the modules in lib
test/lcdb-wf-test unit_tests --pytest
diff --git a/test/lcdb-wf-test b/test/lcdb-wf-test
index fb7adf39..d841290f 100755
--- a/test/lcdb-wf-test
+++ b/test/lcdb-wf-test
@@ -3,19 +3,6 @@
"""
This script aims to make it more convenient to run various tests using
different configs.
-
-data: gets example data
-unit: runs unit tests (pytest, testthat, check urls, check docs)
-workflows: runs workflows and downstream tasks
-
-rnaseq:
- standard:
- desc: "Run main rnaseq workflow. Supply additional snakemake args."
- command: "cd workflows/rnaseq && ./run_test.sh $SNAKEMAKE_ARGS"
- trackhub:
- desc: "Build the trackhub for rnaseq. Requires 'standard' to have been run"
- command: "cd workflows/rnaseq && python rnaseq_trackhub.py config/config.yaml config/hub_config.yaml"
-
"""
import os
import shlex
From c1d0137d84199550b20e1fcee783108fad4f47a1 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Thu, 24 Nov 2022 09:00:26 -0500
Subject: [PATCH 33/91] run set-path on pytest ci job
---
.circleci/config.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index e3ba5d12..84ed9342 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -299,6 +299,7 @@ jobs:
steps:
- checkout
- *restore_cache
+ - *set-path
- *setup
- *pytest-step
From ab339b3405b6da7e92207f125b14b6c258489d69 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Thu, 24 Nov 2022 09:14:43 -0500
Subject: [PATCH 34/91] copy test config for ci
---
.circleci/config.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 84ed9342..caec003b 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -98,6 +98,7 @@ variables:
mkdir $DEPLOY/ci
mkdir $DEPLOY/test
cp test/lcdb-wf-test $DEPLOY/test
+ cp test/workflow_test_params.yaml $DEPLOY/test
cp ci/get-data.py $DEPLOY/ci
# the ./run_test.sh scripts run this
From 0f774da8f9f47b1afe757772442454805f3d8ced Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Thu, 24 Nov 2022 09:36:48 -0500
Subject: [PATCH 35/91] typo in ci config
---
.circleci/config.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index caec003b..587d25ff 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -106,7 +106,7 @@ variables:
# download example data
cd $DEPLOY
- test/lcdb-wf-test data --kinds=all --verbose
+ test/lcdb-wf-test data --kind=all --verbose
# --------------------------------------------------------------------------
# Run the doctests across the included modules
From 62ed17b2fe1bb79b890b3cd7ade851a1354377ff Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Thu, 24 Nov 2022 09:49:44 -0500
Subject: [PATCH 36/91] allow --kind all
---
test/lcdb-wf-test | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/test/lcdb-wf-test b/test/lcdb-wf-test
index d841290f..4a5c251d 100755
--- a/test/lcdb-wf-test
+++ b/test/lcdb-wf-test
@@ -77,7 +77,7 @@ class Runner(object):
parser.add_argument(
"--kind",
default="all",
- choices=["rnaseq", "chipseq"],
+ choices=["all", "rnaseq", "chipseq"],
help="Kind of data to download",
)
parser.add_argument(
From cd8422eff5812d5cdaa820493d1dab5af5ba8357 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Thu, 24 Nov 2022 18:58:02 -0500
Subject: [PATCH 37/91] export $ORIG
---
.circleci/config.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 587d25ff..9e045938 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -54,6 +54,7 @@ variables:
echo 'export LCDBWF_ENV_R=lcdb-wf-test-r' >> $BASH_ENV
echo 'export LC_ALL=en_US.utf8' >> $BASH_ENV
echo 'export LANG=en_US.utf8' >> $BASH_ENV
+ echo 'export ORIG=$(pwd)' >> $BASH_ENV
source $BASH_ENV
# --------------------------------------------------------------------------
# Set up conda if the environments do not already exist
@@ -160,7 +161,6 @@ variables:
run:
name: chipseq misc
command: |
- ORIG=$(pwd)
cd $DEPLOY/workflows/chipseq
source activate lcdb-wf-test
./run_test.sh --use-conda -j2 -k -p -r \
From 03c83dfafd2c493f3ba7551e9f7afa579361bf6b Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Thu, 24 Nov 2022 19:58:25 -0500
Subject: [PATCH 38/91] more test refactoring
---
.circleci/config.yml | 14 +--
test/lcdb-wf-test | 152 ++++++++++++++++++++++++++++-----
test/workflow_test_params.yaml | 12 +--
3 files changed, 139 insertions(+), 39 deletions(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 9e045938..b6111153 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -133,16 +133,6 @@ variables:
test/lcdb-wf-test unit_tests --r-test
- # --------------------------------------------------------------------------
- # Other downstream jobs depend on this so that we can catch trivial errors
- # quickly
- rnaseq-dryrun: &rnaseq-dryrun
- run:
- name: dry run
- command: |
- source activate lcdb-wf-test
- $DEPLOY/test/lcdb-wf-test --rnaseq dryrun
-
# --------------------------------------------------------------------------
# Standard chipseq workflow
chipseq-step: &chipseq-step
@@ -189,9 +179,8 @@ variables:
run:
name: references workflow
command: |
- cd $DEPLOY/workflows/references
source activate lcdb-wf-test
- $DEPLOY/test/lcdb-wf-test --references
+ $DEPLOY/test/lcdb-wf-test references --run-workflow --configfile=config/config.yaml -j2 -p -r -k --orig $ORIG
# --------------------------------------------------------------------------
# Standard RNA-seq workflow
@@ -201,6 +190,7 @@ variables:
command: |
cd $DEPLOY
source activate lcdb-wf-test
+ $DEPLOY/test/lcdb-wf-test rnaseq --run-workflow -n
$DEPLOY/test/lcdb-wf-test rnaseq --run-workflow --use-conda -j2 -k -p -r --orig $ORIG
$DEPLOY/test/lcdb-wf-test rnaseq --trackhub --orig $ORIG
diff --git a/test/lcdb-wf-test b/test/lcdb-wf-test
index 4a5c251d..dcc75a09 100755
--- a/test/lcdb-wf-test
+++ b/test/lcdb-wf-test
@@ -55,7 +55,60 @@ class Runner(object):
def __init__(self):
parser = argparse.ArgumentParser(
- description="Test runner for lcdb-wf",
+ description="""
+ Test runner for lcdb-wf. There are many things to test; as a first pass use
+ these with appropriate Snakemake args (-n, -j, --use-conda, etc)
+
+ %(prog)s data --kind all
+ %(prog)s unit_tests --pytest
+ %(prog)s unit_tests --r-test
+ %(prog)s rnaseq --run-workflow
+ %(prog)s rnaseq --trackhub
+ %(prog)s rnaseq --downstream
+ %(prog)s chipseq --run-workflow
+ %(prog)s references --run-workflow --configfile=config/config.yaml
+
+ DATA
+ ----
+ %(prog)s data --kind all --verbose
+
+ UNIT TESTS
+ ----------
+ # Run the pytest unit tests on the lib/
+ %(prog)s unit_tests --pytest
+
+ # Run tests on lcdbwf R package
+ %(prog)s unit_tests --r-test
+
+ # Ensure URLs in the configs exist
+ %(prog)s unit_tests --url-check
+
+ # Ensure rnaseq.Rmd has matching sections in the docs
+ %(prog)s unit_tests --ensure-docs
+
+ RNASEQ
+ ------
+ # Run main workflow
+ %(prog)s rnaseq --run-workflow
+
+ # Build RNA-seq trackhub from output of main workflow
+ %(prog)s rnaseq --trackhub
+
+ # Run rnaseq.Rmd
+ %(prog)s rnaseq --downstream
+
+ # Each of these runs a restricted subset of the workflow with
+ # customized configs; they should be run one at a time.
+ %(prog)s rnaseq --run-workflow --sra-pe
+ %(prog)s rnaseq --run-workflow --sra-se
+ %(prog)s rnaseq --run-workflow --strandedness-pe
+ %(prog)s rnaseq --run-workflow --strandedness-se
+ %(prog)s rnaseq --run-workflow --star-2pass
+ %(prog)s rnaseq --run-workflow --star-1pass
+ %(prog)s rnaseq --run-workflow --pe
+
+ """,
+ formatter_class=argparse.RawDescriptionHelpFormatter
)
choices = [i.replace("_cmd_", "") for i in dir(self) if i.startswith("_cmd_")]
@@ -272,7 +325,7 @@ class Runner(object):
# attribute.
group = parser.add_mutually_exclusive_group()
workflow_prefix = "bash run_test.sh"
- workflow_dir = "workflow/rnaseq"
+ workflow_dir = TOPLEVEL / "workflows/rnaseq"
for key, val in WORKFLOW_ARGS["rnaseq"].items():
group.add_argument(
"--" + key,
@@ -295,11 +348,17 @@ class Runner(object):
extra = [i.replace("__ORIG__", args.orig) for i in extra]
strargs = " ".join(extra)
- print_header(f"Running workflows/rnaseq/run_test.sh with args: {strargs}")
+ cmd = (
+ 'eval "$(conda shell.bash hook)" '
+ f"&& conda activate {args.env} "
+ f"&& (cd {workflow_dir} && {workflow_prefix} {strargs})"
+ )
+ print_header(f"Running the following command:\n{cmd}")
sp.run(
- shlex.split(workflow_prefix) + extra,
- cwd=TOPLEVEL / "workflows/rnaseq",
+ cmd,
check=True,
+ shell=True,
+ executable="/bin/bash"
)
if args.trackhub:
print_header("running trackhub script")
@@ -326,24 +385,75 @@ class Runner(object):
executable="/bin/bash"
)
+ def _cmd_chipseq(self):
+ """
+ This function handles the "chipseq" subcommand.
+ """
+
+ parser = argparse.ArgumentParser(
+ description="Run chipseq workflow",
+ parents=[self.global_parser],
+ )
+ parser.add_argument(
+ "--run-workflow",
+ action="store_true",
+ help="""Run chipseq workflow using the run_tesh.sh harness, which
+ edits the Snakefile to use test settings before running. Additional
+ args not specified here are passed to Snakemake, or use other flags
+ below to easily specify config sets.""",
+ )
+ args, extra = parser.parse_known_args(sys.argv[2:])
+ workflow_prefix = "bash run_test.sh"
+ workflow_dir = TOPLEVEL / "workflows/chipseq"
+ if args.run_workflow:
+ extra = [i.replace("__ORIG__", args.orig) for i in extra]
+ strargs = " ".join(extra)
+ cmd = (
+ 'eval "$(conda shell.bash hook)" '
+ f"&& conda activate {args.env} "
+ f"&& (cd {workflow_dir} && {workflow_prefix} {strargs})"
+ )
+ print_header(f"Running the following command:\n{cmd}")
+ sp.run(
+ cmd,
+ shell=True,
+ check=True,
+ executable="/bin/bash"
+ )
+
+ def _cmd_references(self):
+ parser = argparse.ArgumentParser(
+ description="Run references workflow",
+ parents=[self.global_parser],
+ )
+ parser.add_argument(
+ "--run-workflow",
+ action="store_true",
+ help="""Run references workflow using the run_tesh.sh harness, which
+ edits the Snakefile to use test settings before running."""
+ )
+ args, extra = parser.parse_known_args(sys.argv[2:])
+
+ workflow_prefix = "bash run_test.sh"
+ workflow_dir = TOPLEVEL / "workflows/references"
+ if args.run_workflow:
+ extra = [i.replace("__ORIG__", args.orig) for i in extra]
+ strargs = " ".join(extra)
+ cmd = (
+ 'eval "$(conda shell.bash hook)" '
+ f"&& conda activate {args.env} "
+ f"&& (cd {workflow_dir} && {workflow_prefix} {strargs})"
+ )
+ print_header(f"Running the following command:\n{cmd}")
+ sp.run(
+ cmd,
+ shell=True,
+ check=True,
+ executable="/bin/bash"
+ )
+
if __name__ == "__main__":
Runner()
-if __name__ == "__mn__":
- if args.references:
- print_header("references")
- snakefile(
- "workflows/references",
- snakemake_args=[
- "--use-conda",
- "-j",
- args.cpus,
- "-k",
- "-p",
- "-r",
- "--configfile",
- "config/config.yaml",
- ],
- )
# vim: ft=python
diff --git a/test/workflow_test_params.yaml b/test/workflow_test_params.yaml
index f04cfe40..70e57da6 100644
--- a/test/workflow_test_params.yaml
+++ b/test/workflow_test_params.yaml
@@ -59,9 +59,9 @@ rnaseq:
__ORIG__/test/test_configs/star_override_1pass.yaml
--config sampletable=__ORIG__/test/test_configs/star_1pass.tsv
-pe:
- desc: Tests paired-end data
- args: |
- --until multiqc
- --configfile __ORIG__/test/test_configs/test_rnaseq_config.yaml
- --config sampletable=__ORIG__/test/test_configs/test_pe_sampletable.tsv
+ pe:
+ desc: Tests paired-end data
+ args: |
+ --until multiqc
+ --configfile __ORIG__/test/test_configs/test_rnaseq_config.yaml
+ --config sampletable=__ORIG__/test/test_configs/test_pe_sampletable.tsv
From 7fb9b9b8af376f2af97aa795853d95a41672bd33 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Fri, 25 Nov 2022 08:27:20 -0500
Subject: [PATCH 39/91] test infra updates
---
.circleci/config.yml | 5 +++--
test/lcdb-wf-test | 39 +++++++++++++++++++++++++++++++--------
2 files changed, 34 insertions(+), 10 deletions(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index b6111153..47d09373 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -141,8 +141,9 @@ variables:
command: |
cd $DEPLOY/workflows/chipseq
source activate lcdb-wf-test
- ./run_test.sh --use-conda -j2 -k -p -r
- python chipseq_trackhub.py config/config.yaml config/hub_config.yaml
+ $DEPLOY/test/lcdb-wf-test chipseq --run-workflow --use-conda -j2 -k -p -r
+ $DEPLOY/test/lcdb-wf-test chipseq --trackhub
+
# --------------------------------------------------------------------------
# Previous versions had an error where chipseq peaks needed to be defined for
# every caller. This does a (relatively) quick test to only run a single
diff --git a/test/lcdb-wf-test b/test/lcdb-wf-test
index dcc75a09..9b14523d 100755
--- a/test/lcdb-wf-test
+++ b/test/lcdb-wf-test
@@ -361,16 +361,19 @@ class Runner(object):
executable="/bin/bash"
)
if args.trackhub:
- print_header("running trackhub script")
+ cmd = (
+ 'eval "$(conda shell.bash hook)" '
+ f"&& conda activate {args.env} "
+ f"&& (cd {workflow_dir} "
+ "&& python rnaseq_trackhub config/config.yaml config/hub_config.yaml)"
+ )
+ print_header(f"Building trackhub with command: {cmd}")
+
sp.run(
- [
- "python",
- "rnaseq_trackhub.py",
- "config/config.yaml",
- "config/hub_config.yaml",
- ],
+ cmd,
+ shell=True,
check=True,
- cwd="workflows/rnaseq",
+ executable="/bin/bash"
)
print("See workflows/rnaseq/staging for the built trackhub")
@@ -402,9 +405,13 @@ class Runner(object):
args not specified here are passed to Snakemake, or use other flags
below to easily specify config sets.""",
)
+ parser.add_argument(
+ "--trackhub", action="store_true", help="Build the rnaseq track hub"
+ )
args, extra = parser.parse_known_args(sys.argv[2:])
workflow_prefix = "bash run_test.sh"
workflow_dir = TOPLEVEL / "workflows/chipseq"
+
if args.run_workflow:
extra = [i.replace("__ORIG__", args.orig) for i in extra]
strargs = " ".join(extra)
@@ -420,6 +427,22 @@ class Runner(object):
check=True,
executable="/bin/bash"
)
+ if args.trackhub:
+ cmd = (
+ 'eval "$(conda shell.bash hook)" '
+ f"&& conda activate {args.env} "
+ f"&& (cd {workflow_dir} "
+ "&& python chipseq_trackhub config/config.yaml config/hub_config.yaml)"
+ )
+ print_header(f"Building trackhub with command: {cmd}")
+
+ sp.run(
+ cmd,
+ shell=True,
+ check=True,
+ executable="/bin/bash"
+ )
+ print("See workflows/chipseq/staging for the built trackhub")
def _cmd_references(self):
parser = argparse.ArgumentParser(
From 32a42280888fe99e08e58d30a483004eb052214b Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Fri, 25 Nov 2022 08:45:15 -0500
Subject: [PATCH 40/91] typo
---
test/lcdb-wf-test | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/test/lcdb-wf-test b/test/lcdb-wf-test
index 9b14523d..375c921a 100755
--- a/test/lcdb-wf-test
+++ b/test/lcdb-wf-test
@@ -365,7 +365,7 @@ class Runner(object):
'eval "$(conda shell.bash hook)" '
f"&& conda activate {args.env} "
f"&& (cd {workflow_dir} "
- "&& python rnaseq_trackhub config/config.yaml config/hub_config.yaml)"
+ "&& python rnaseq_trackhub.py config/config.yaml config/hub_config.yaml)"
)
print_header(f"Building trackhub with command: {cmd}")
@@ -432,7 +432,7 @@ class Runner(object):
'eval "$(conda shell.bash hook)" '
f"&& conda activate {args.env} "
f"&& (cd {workflow_dir} "
- "&& python chipseq_trackhub config/config.yaml config/hub_config.yaml)"
+ "&& python chipseq_trackhub.py config/config.yaml config/hub_config.yaml)"
)
print_header(f"Building trackhub with command: {cmd}")
From 92b7fc05d11d8d50e5d25da41508e5272b0643ea Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Fri, 25 Nov 2022 15:46:23 -0500
Subject: [PATCH 41/91] debug test
---
.circleci/config.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 47d09373..32013571 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -63,6 +63,7 @@ variables:
name: Setup conda
command: |
set -e
+ echo $LCDBWF_ENV
# We only do the installation if the conda environment does not already
# exist.
if ! conda env list | grep -q "lcdb-wf-test"; then
From 8c39c3ff4fbdc34bd40946a05571882bb0261da9 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Fri, 25 Nov 2022 15:49:45 -0500
Subject: [PATCH 42/91] debug test
---
.circleci/config.yml | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 32013571..4825981a 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -63,7 +63,6 @@ variables:
name: Setup conda
command: |
set -e
- echo $LCDBWF_ENV
# We only do the installation if the conda environment does not already
# exist.
if ! conda env list | grep -q "lcdb-wf-test"; then
@@ -71,6 +70,8 @@ variables:
conda config --system --add channels defaults
conda config --system --add channels bioconda
conda config --system --add channels conda-forge
+ echo "env: $LCDBWF_ENV"
+ echo "env-r: $LCDBWF_ENV_R"
conda install mamba -y
mamba env create -n $LCDBWF_ENV --file env.yml
mamba env create -n $LCDBWF_ENV_R --file env-r.yml
From 82e0e96457fa2270473b79214901e4302c6cafe0 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Fri, 25 Nov 2022 15:51:56 -0500
Subject: [PATCH 43/91] debug test
---
.circleci/config.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 4825981a..e9c9dfd2 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -63,6 +63,7 @@ variables:
name: Setup conda
command: |
set -e
+ source $BASH_ENV
# We only do the installation if the conda environment does not already
# exist.
if ! conda env list | grep -q "lcdb-wf-test"; then
From 3c32959fe4e4326a47570b7d2659feeca6712a1d Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Fri, 25 Nov 2022 15:59:03 -0500
Subject: [PATCH 44/91] debug test
---
.circleci/config.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index e9c9dfd2..e72a90f1 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -264,6 +264,7 @@ jobs:
<<: *defaults
steps:
- checkout
+ - *set-path
# Check the hashes of requirements files. If they match a cache, load it.
# The cache is set up to be the entire miniconda installation, so that
From ea7558f885a76686778bb6cea5149d47cec9266f Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Fri, 25 Nov 2022 16:28:06 -0500
Subject: [PATCH 45/91] debug test
---
.circleci/config.yml | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index e72a90f1..2deb6683 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -49,6 +49,7 @@ variables:
command: |
# x11-utils required to avoid R::png() segfaulting
apt update && apt install -y locales-all locales rsync x11-utils
+ conda install -y yaml
echo 'export DEPLOY=/tmp/lcdb-wf-test' >> $BASH_ENV
echo 'export LCDBWF_ENV=lcdb-wf-test' >> $BASH_ENV
echo 'export LCDBWF_ENV_R=lcdb-wf-test-r' >> $BASH_ENV
@@ -71,9 +72,7 @@ variables:
conda config --system --add channels defaults
conda config --system --add channels bioconda
conda config --system --add channels conda-forge
- echo "env: $LCDBWF_ENV"
- echo "env-r: $LCDBWF_ENV_R"
- conda install mamba -y
+ conda install mamba yaml -y
mamba env create -n $LCDBWF_ENV --file env.yml
mamba env create -n $LCDBWF_ENV_R --file env-r.yml
fi
From c836e91c6499c6a76521b5931141765f38ac5b89 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Fri, 25 Nov 2022 16:46:15 -0500
Subject: [PATCH 46/91] debug test
---
.circleci/config.yml | 5 -----
1 file changed, 5 deletions(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 2deb6683..f2112515 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -198,11 +198,6 @@ variables:
$DEPLOY/test/lcdb-wf-test rnaseq --trackhub --orig $ORIG
- # Starting in v1.6, we separate out the non-R from the
- # R environments. So we need to test the rnaseq.Rmd separately
- # outside the context of the Snakefile.
- source activate lcdb-wf-test-r
-
# This run the preprocessor on the Rmd files and stores them
# in a new download-test directory (see the comments in the script
# for details)
From 04f01fab708699bb9ee5b8d86a4dc29ddfed6943 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Fri, 25 Nov 2022 17:29:42 -0500
Subject: [PATCH 47/91] debug test
---
.circleci/config.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index f2112515..d5d62086 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -204,7 +204,7 @@ variables:
$DEPLOY/test/lcdb-wf-test rnaseq --downstream
# bundle up the entire directory to be used as an artifact
- tar -zcf downstream.tar.gz downstream-test/
+ tar -zcf downstream.tar.gz workflows/rnaseq/downstream-test/
# --------------------------------------------------------------------------
# Various tests on RNA-seq workflow that don't warrant the overhead of a new
From 54bf20e10be9539a90300f59150d402b130c133e Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Fri, 25 Nov 2022 21:39:24 -0500
Subject: [PATCH 48/91] typo in wrapper_slurm
---
include/WRAPPER_SLURM | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/include/WRAPPER_SLURM b/include/WRAPPER_SLURM
index bed1df6d..09590f4b 100755
--- a/include/WRAPPER_SLURM
+++ b/include/WRAPPER_SLURM
@@ -2,7 +2,7 @@
#SBATCH --job-name="lcdb-wf"
#SBATCH --partition="norm"
#SBATCH --time=12:00:00
-#SBATHC --gres=lscratch:5
+#SBATCH --gres=lscratch:5
# make logdir
if [[ ! -e logs ]]; then mkdir -p logs; fi
From c457320958cd49c03f5e5eaa10a88ae04c96062a Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Sat, 26 Nov 2022 10:01:37 -0500
Subject: [PATCH 49/91] remove shell prefix setup
---
workflows/rnaseq/Snakefile | 5 -----
1 file changed, 5 deletions(-)
diff --git a/workflows/rnaseq/Snakefile b/workflows/rnaseq/Snakefile
index a41b28e9..7b6e3d8a 100644
--- a/workflows/rnaseq/Snakefile
+++ b/workflows/rnaseq/Snakefile
@@ -23,11 +23,6 @@ config = common.load_config(config)
include: '../references/Snakefile'
-shell.prefix(
- 'set -euo pipefail; export R_PROFILE_USER=; export TMPDIR={};'
- .format(cluster_specific.tempdir_for_biowulf())
-)
-shell.executable('/bin/bash')
# Verify configuration of config and sampletable files
helpers.preflight(config)
From d539abf635b7e14bebe44b53dffd17c7d24ffcfc Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Sat, 26 Nov 2022 10:03:07 -0500
Subject: [PATCH 50/91] add resources to rnaseq rules
---
workflows/rnaseq/Snakefile | 142 ++++++++++++++++++++++++++++++++-----
1 file changed, 123 insertions(+), 19 deletions(-)
diff --git a/workflows/rnaseq/Snakefile b/workflows/rnaseq/Snakefile
index 7b6e3d8a..cbef1644 100644
--- a/workflows/rnaseq/Snakefile
+++ b/workflows/rnaseq/Snakefile
@@ -23,6 +23,13 @@ config = common.load_config(config)
include: '../references/Snakefile'
+def autobump(value):
+ """
+ Increments value for each attempt.
+ """
+ def f(wildcards, attempt):
+ return attempt * value
+ return f
# Verify configuration of config and sampletable files
helpers.preflight(config)
@@ -77,7 +84,7 @@ rule targets:
if 'orig_filename' in c.sampletable.columns:
- localrules: symlinks
+ localrules: symlinks, symlink_targets
# Convert the sampletable to be indexed by the first column, for
# convenience in generating the input/output filenames.
@@ -101,6 +108,10 @@ if 'orig_filename' in c.sampletable.columns:
orig_for_sample
output:
render_r1_r2(c.patterns['fastq'])
+ threads: 1
+ resources:
+ mem_mb=100,
+ runtime=10,
run:
assert len(output) == len(input), (input, output)
for src, linkname in zip(input, output):
@@ -126,6 +137,9 @@ if 'Run' in c.sampletable.columns and sum(c.sampletable['Run'].str.startswith('S
is_paired=c.is_paired,
sampletable=_st,
# limit = 100000, # [TEST SETTINGS]
+ resources:
+ mem_mb=1024,
+ runtime=autobump(120)
conda:
'../../wrappers/wrappers/fastq-dump/environment.yaml'
script:
@@ -147,6 +161,9 @@ rule sample_strand_check:
log:
c.patterns['strand_check']['tsv'] + '.log'
threads: 6
+ resources:
+ mem_mb=1024 * 8,
+ runtime=autobump(120)
run:
prefix = aligners.prefix_from_bowtie2_index(input.index)
nreads = int(config['strand_check_reads']) * 4
@@ -183,6 +200,9 @@ rule strand_check:
filelist=temporary('strand_check/filelist')
log:
'strand_check/strandedness.log'
+ resources:
+ mem_mb=1024 * 1,
+ runtime=autobump(120)
run:
with open(output.filelist, 'w') as fout:
for i in input:
@@ -207,6 +227,9 @@ rule cutadapt:
log:
render_r1_r2(c.patterns['cutadapt'])[0] + '.log'
threads: 6
+ resources:
+ mem_mb=1024 * 2,
+ runtime=autobump(120)
run:
# NOTE: Change cutadapt params here
@@ -248,6 +271,9 @@ rule fastqc:
output:
html='{sample_dir}/{sample}/fastqc/{sample}{suffix}_fastqc.html',
zip='{sample_dir}/{sample}/fastqc/{sample}{suffix}_fastqc.zip',
+ resources:
+ mem_mb=1024 * 2,
+ runtime=autobump(120)
script:
wrapper_for('fastqc/wrapper.py')
@@ -265,6 +291,9 @@ if config['aligner']['index'] == 'hisat2':
log:
c.patterns['bam'] + '.log'
threads: 6
+ resources:
+ mem_mb=1024 * 32,
+ runtime=autobump(120)
run:
prefix = aligners.prefix_from_bowtie2_index(input.index)
sam = output.bam.replace('.bam', '.sam')
@@ -337,6 +366,9 @@ if config['aligner']['index'] == 'star':
log:
c.patterns['bam'].replace('.bam', '.star.bam.log')
threads: 16
+ resources:
+ mem_mb=1024 * 64,
+ runtime=autobump(120)
run:
genomedir = os.path.dirname(input.index[0])
outdir = os.path.dirname(output[0])
@@ -369,6 +401,9 @@ if config['aligner']['index'] == 'star-twopass':
log:
c.patterns['bam'].replace('.bam', '.star-pass1.bam.log')
threads: 16
+ resources:
+ mem_mb=1024 * 64,
+ runtime=autobump(120)
run:
genomedir = os.path.dirname(input.index[0])
outdir = os.path.dirname(output[0])
@@ -406,6 +441,9 @@ if config['aligner']['index'] == 'star-twopass':
log:
c.patterns['bam'].replace('.bam', '.star-pass2.bam.log')
threads: 16
+ resources:
+ mem_mb=1024 * 64,
+ runtime=autobump(120)
run:
genomedir = os.path.dirname(input.index[0])
outdir = os.path.dirname(output[0])
@@ -444,6 +482,9 @@ rule rRNA:
log:
c.patterns['rrna']['bam'] + '.log'
threads: 6
+ resources:
+ mem_mb=1024 * 2,
+ runtime=autobump(120)
run:
prefix = aligners.prefix_from_bowtie2_index(input.index)
sam = output.bam.replace('.bam', '.sam')
@@ -474,6 +515,10 @@ rule fastq_count:
fastq='{sample_dir}/{sample}/{sample}{suffix}.fastq.gz'
output:
'{sample_dir}/{sample}/{sample}{suffix}.fastq.gz.libsize'
+ threads: 1
+ resources:
+ mem_mb=1024 * 1,
+ runtime=autobump(120)
shell:
'zcat {input} | echo $((`wc -l`/4)) > {output}'
@@ -486,6 +531,10 @@ rule bam_count:
bam='{sample_dir}/{sample}/{suffix}.bam'
output:
'{sample_dir}/{sample}/{suffix}.bam.libsize'
+ threads: 1
+ resources:
+ mem_mb=1024 * 2,
+ runtime=autobump(120)
shell:
'samtools view -c {input} > {output}'
@@ -498,6 +547,10 @@ rule bam_index:
bam='{prefix}.bam'
output:
bai='{prefix}.bam.bai'
+ threads: 1
+ resources:
+ mem_mb=1024 * 2,
+ runtime=autobump(120)
shell:
'samtools index {input} {output}'
@@ -524,6 +577,10 @@ rule fastq_screen:
txt=c.patterns['fastq_screen']
log:
c.patterns['fastq_screen'] + '.log'
+ threads: 6
+ resources:
+ mem_mb=1024 * 4,
+ runtime=autobump(120)
params: subset=100000
script:
wrapper_for('fastq_screen/wrapper.py')
@@ -541,6 +598,9 @@ rule featurecounts:
log:
'{sample_dir}/rnaseq_aggregation/featurecounts.txt.log'
threads: 8
+ resources:
+ mem_mb=1024 * 2,
+ runtime=autobump(120)
run:
# NOTE: By default, we use -p for paired-end
p_arg = ''
@@ -577,6 +637,10 @@ rule rrna_libsizes_table:
output:
json=c.patterns['rrna_percentages_yaml'],
tsv=c.patterns['rrna_percentages_table']
+ threads: 1
+ resources:
+ mem_mb=1024 * 2,
+ runtime=autobump(120)
run:
def rrna_sample(f):
return helpers.extract_wildcards(c.patterns['rrna']['libsize'], f)['sample']
@@ -641,6 +705,10 @@ rule multiqc:
config='config/multiqc_config.yaml'
output: c.targets['multiqc']
log: c.targets['multiqc'][0] + '.log'
+ threads: 1
+ resources:
+ mem_mb=1024 * 2,
+ runtime=autobump(120)
run:
analysis_directory = set([os.path.dirname(i) for i in input])
outdir = os.path.dirname(c.targets['multiqc'][0])
@@ -675,6 +743,11 @@ rule markduplicates:
# config.
java_args='-Xmx20g'
# java_args='-Xmx2g' # [TEST SETTINGS -1]
+ threads: 1
+ resources:
+ mem_mb=1024 * 32,
+ runtime=autobump(120),
+ disk_mb=1024 *100
shell:
'picard '
'{params.java_args} '
@@ -703,6 +776,10 @@ rule collectrnaseqmetrics:
# java_args='-Xmx2g' # [TEST SETTINGS -1]
log:
c.patterns['collectrnaseqmetrics']['metrics'] + '.log'
+ threads: 1
+ resources:
+ mem_mb=1024 * 32,
+ runtime=autobump(120)
run:
strand_arg = helpers.strand_arg_lookup(
c, {
@@ -732,6 +809,10 @@ rule preseq:
bam=c.patterns['bam']
output:
c.patterns['preseq']
+ threads: 1
+ resources:
+ mem_mb=1024 * 1,
+ runtime=autobump(120)
shell:
'preseq '
'c_curve '
@@ -754,6 +835,9 @@ rule salmon:
log:
c.patterns['salmon'] + '.log'
threads: 6
+ resources:
+ mem_mb=1024 * 32,
+ runtime=autobump(120)
run:
if c.is_paired:
fastq_arg = f'-1 {input.fastq[0]} -2 {input.fastq[1]} '
@@ -794,6 +878,9 @@ rule kallisto:
c.patterns['kallisto'] + '.log'
threads:
8
+ resources:
+ mem_mb=1024 * 32,
+ runtime=autobump(120)
run:
if c.is_paired:
se_args = ''
@@ -837,6 +924,9 @@ rule rseqc_infer_experiment:
txt=c.patterns['rseqc']['infer_experiment']
log:
c.patterns['rseqc']['infer_experiment'] + '.log'
+ resources:
+ mem_mb=1024 * 2,
+ runtime=autobump(120)
shell:
'infer_experiment.py -r {input.bed12} -i {input.bam} > {output} &> {log}'
@@ -852,10 +942,33 @@ rule rseqc_read_distribution:
txt=c.patterns['rseqc']['read_distribution']
log:
c.patterns['rseqc']['read_distribution'] + '.log'
+ resources:
+ mem_mb=1024 * 2,
+ runtime=autobump(120)
shell:
'read_distribution.py -i {input.bam} -r {input.bed12} > {output} &> {log}'
+rule idxstats:
+ """
+ Run samtools idxstats on sample bams
+ """
+ input:
+ bam=c.patterns['markduplicates']['bam'],
+ bai=c.patterns['markduplicates']['bam'] + '.bai'
+ output:
+ txt=c.patterns['samtools']['idxstats']
+ log:
+ c.patterns['samtools']['idxstats'] + '.log'
+ resources:
+ mem_mb=1024 * 16,
+ runtime=autobump(120)
+ run:
+ shell(
+ 'samtools idxstats {input.bam} 2> {log} 1> {output.txt}'
+ )
+
+
# Common arguments used for bamCoverage rules below
BAMCOVERAGE_ARGS = (
'--minMappingQuality 20 ' # excludes multimappers
@@ -872,6 +985,9 @@ rule bigwig_neg:
bai=c.patterns['markduplicates']['bam'] + '.bai',
output: c.patterns['bigwig']['neg']
threads: 8
+ resources:
+ mem_mb=1024 * 16,
+ runtime=autobump(120)
log:
c.patterns['bigwig']['neg'] + '.log'
run:
@@ -902,6 +1018,9 @@ rule bigwig_pos:
bai=c.patterns['markduplicates']['bam'] + '.bai',
output: c.patterns['bigwig']['pos']
threads: 8
+ resources:
+ mem_mb=1024 * 16,
+ runtime=autobump(120)
log:
c.patterns['bigwig']['pos'] + '.log'
@@ -950,6 +1069,9 @@ if 'merged_bigwigs' in config:
c.patterns['merged_bigwig']
log:
c.patterns['merged_bigwig'] + '.log'
+ resources:
+ mem_mb=1024 * 16,
+ runtime=autobump(120)
script:
wrapper_for('average-bigwigs/wrapper.py')
@@ -975,22 +1097,4 @@ rule rnaseq_rmarkdown:
'> {log} 2>&1'
# [TEST_SETTINGS -1]
-
-rule idxstats:
- """
- Run samtools idxstats on sample bams
- """
- input:
- bam=c.patterns['markduplicates']['bam'],
- bai=c.patterns['markduplicates']['bam'] + '.bai'
- output:
- txt=c.patterns['samtools']['idxstats']
- log:
- c.patterns['samtools']['idxstats'] + '.log'
- run:
- shell(
- 'samtools idxstats {input.bam} 2> {log} 1> {output.txt}'
- )
-
-
# vim: ft=python
From 1799f0f5b9e8940bb8f70b7edc3f7a63898bbcdc Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Sat, 26 Nov 2022 10:19:02 -0500
Subject: [PATCH 51/91] rm shell prefix from rnaseq
---
workflows/rnaseq/Snakefile | 5 -----
1 file changed, 5 deletions(-)
diff --git a/workflows/rnaseq/Snakefile b/workflows/rnaseq/Snakefile
index a41b28e9..7b6e3d8a 100644
--- a/workflows/rnaseq/Snakefile
+++ b/workflows/rnaseq/Snakefile
@@ -23,11 +23,6 @@ config = common.load_config(config)
include: '../references/Snakefile'
-shell.prefix(
- 'set -euo pipefail; export R_PROFILE_USER=; export TMPDIR={};'
- .format(cluster_specific.tempdir_for_biowulf())
-)
-shell.executable('/bin/bash')
# Verify configuration of config and sampletable files
helpers.preflight(config)
From 22a5f69bf0fc356f54ab32e1bbfb5dbccb032672 Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Wed, 22 Feb 2023 16:11:03 -0500
Subject: [PATCH 52/91] remove clusterconfig and cluster from WRAPPER_SLURM
---
include/WRAPPER_SLURM | 2 --
1 file changed, 2 deletions(-)
diff --git a/include/WRAPPER_SLURM b/include/WRAPPER_SLURM
index 09590f4b..5151e141 100755
--- a/include/WRAPPER_SLURM
+++ b/include/WRAPPER_SLURM
@@ -16,8 +16,6 @@ if [[ ! -e logs ]]; then mkdir -p logs; fi
--rerun-incomplete \
--jobname "s.{rulename}.{jobid}.sh" \
-j 999 \
- --cluster-config config/clusterconfig.yaml \
- --cluster 'sbatch {cluster.prefix} --cpus-per-task={threads} --output=logs/{rule}.o.%j --error=logs/{rule}.e.%j' \
--use-conda \
--configfile config/config.yaml \
--latency-wait=300 \
From e26bde8f85753eb4ae0a20df9003b8c7869eca38 Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Thu, 23 Feb 2023 13:37:20 -0500
Subject: [PATCH 53/91] use snakemake profile env var if set
---
include/WRAPPER_SLURM | 17 +++++++++++++++++
1 file changed, 17 insertions(+)
diff --git a/include/WRAPPER_SLURM b/include/WRAPPER_SLURM
index 5151e141..e598572c 100755
--- a/include/WRAPPER_SLURM
+++ b/include/WRAPPER_SLURM
@@ -7,6 +7,22 @@
# make logdir
if [[ ! -e logs ]]; then mkdir -p logs; fi
+# use SNAKEMAKE_PROFILE if one is set in the environment variables
+if [ -z "$LCDBWF_SNAKE_PROFILE" ]; then
+ if [ -z "$SNAKEMAKE_PROFILE" ]; then
+ # no snakemake profile found
+ PROFILE_CMD=""
+ echo "No environment variable SNAKEMAKE_PROFILE or LCDBWF_SNAKE_PROFILE found."
+ echo "snakemake will run in single job."
+ else
+ # generic SNAKEMAKE_PROFILE found
+ PROFILE_CMD="--profile $SNAKEMAKE_PROFILE"
+ fi
+else
+# LCDBWF_SNAKE_PROFILE found, this takes priority if both profile variables are set
+PROFILE_CMD="--profile $LCDBWF_SNAKE_PROFILE"
+fi
+
# Run snakemake
(
time snakemake \
@@ -18,6 +34,7 @@ if [[ ! -e logs ]]; then mkdir -p logs; fi
-j 999 \
--use-conda \
--configfile config/config.yaml \
+ $PROFILE_CMD \
--latency-wait=300 \
--max-jobs-per-second 1 \
--max-status-checks-per-second 0.01 \
From 46e42262356f3b71cd03400e5cf3ba681162b0c8 Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Thu, 23 Feb 2023 15:30:19 -0500
Subject: [PATCH 54/91] update chipseq Snakefile for snakemake profile
---
workflows/chipseq/Snakefile | 98 +++++++++++++++++++++++++++++++++++--
1 file changed, 93 insertions(+), 5 deletions(-)
diff --git a/workflows/chipseq/Snakefile b/workflows/chipseq/Snakefile
index 532bceae..18a9bb27 100644
--- a/workflows/chipseq/Snakefile
+++ b/workflows/chipseq/Snakefile
@@ -24,11 +24,13 @@ config = common.load_config(config)
include: '../references/Snakefile'
-shell.prefix(
- 'set -euo pipefail; export R_PROFILE_USER=; export TMPDIR={};'
- .format(cluster_specific.tempdir_for_biowulf())
-)
-shell.executable('/bin/bash')
+def autobump(value):
+ """
+ Increments value for each attempt.
+ """
+ def f(wildcards, attempt):
+ return attempt * value
+ return f
# Verify configuration of config and sampletable files
helpers.preflight(config)
@@ -114,6 +116,10 @@ if 'orig_filename' in c.sampletable.columns:
orig_for_sample
output:
render_r1_r2(c.patterns['fastq'])
+ threads: 1
+ resources:
+ mem_mb=100,
+ runtime=10,
run:
assert len(output) == len(input), (input, output)
for src, linkname in zip(input, output):
@@ -139,6 +145,9 @@ if 'Run' in c.sampletable.columns and sum(c.sampletable['Run'].str.startswith('S
is_paired=c.is_paired,
sampletable=_st,
# limit = 100000, # [TEST SETTINGS]
+ resources:
+ mem_mb=autobump(1024),
+ runtime=autobump(120)
conda:
'../../wrappers/wrappers/fastq-dump/environment.yaml'
script:
@@ -152,6 +161,9 @@ rule cutadapt:
fastq=render_r1_r2(c.patterns['fastq'])
output:
fastq=render_r1_r2(c.patterns['cutadapt'])
+ resources:
+ mem_mb=1024 * 2,
+ runtime=autobump(120)
log:
render_r1_r2(c.patterns['cutadapt'])[0] + '.log'
threads: 6
@@ -196,6 +208,9 @@ rule fastqc:
output:
html='{sample_dir}/{sample}/fastqc/{sample}{suffix}_fastqc.html',
zip='{sample_dir}/{sample}/fastqc/{sample}{suffix}_fastqc.zip',
+ resources:
+ mem_mb=1024 * 2,
+ runtime=autobump(120)
script:
wrapper_for('fastqc/wrapper.py')
@@ -212,6 +227,9 @@ rule bowtie2:
log:
c.patterns['bam'] + '.log'
threads: 16
+ resources:
+ mem_mb=1024 * 32,
+ runtime=autobump(120)
run:
prefix = aligners.prefix_from_bowtie2_index(input.index)
sam = output.bam.replace('.bam', '.sam')
@@ -248,6 +266,10 @@ rule unique:
c.patterns['bam']
output:
c.patterns['unique']
+ threads: 1
+ resources:
+ mem_mb=1024,
+ runtime=autobump(120)
shell:
# NOTE: the quality score chosen here should reflect the scores output
# by the aligner used. For example, STAR uses 255 as max mapping
@@ -263,6 +285,10 @@ rule fastq_count:
fastq='{sample_dir}/{sample}/{sample}{suffix}.fastq.gz'
output:
'{sample_dir}/{sample}/{sample}{suffix}.fastq.gz.libsize'
+ threads: 1
+ resources:
+ mem_mb=1024 * 1,
+ runtime=autobump(120)
shell:
'zcat {input} | echo $((`wc -l`/4)) > {output}'
@@ -275,6 +301,10 @@ rule bam_count:
bam='{sample_dir}/{sample}/{suffix}.bam'
output:
'{sample_dir}/{sample}/{suffix}.bam.libsize'
+ threads: 1
+ resources:
+ mem_mb=1024 * 2,
+ runtime=autobump(120)
shell:
'samtools view -c {input} > {output}'
@@ -287,6 +317,10 @@ rule bam_index:
bam='{prefix}.bam'
output:
bai='{prefix}.bam.bai'
+ threads: 1
+ resources:
+ mem_mb=1024 * 2,
+ runtime=autobump(120)
shell:
'samtools index {input} {output}'
@@ -313,6 +347,10 @@ rule fastq_screen:
txt=c.patterns['fastq_screen']
log:
c.patterns['fastq_screen'] + '.log'
+ threads: 6
+ resources:
+ mem_mb=autobump(1024 * 4),
+ runtime=autobump(120)
params: subset=100000
script:
wrapper_for('fastq_screen/wrapper.py')
@@ -345,6 +383,10 @@ rule multiqc:
c.targets['multiqc']
log:
c.targets['multiqc'][0] + '.log'
+ threads: 1
+ resources:
+ mem_mb=1024 * 2,
+ runtime=autobump(120)
run:
analysis_directory = set([os.path.dirname(i) for i in input])
outdir = os.path.dirname(c.targets['multiqc'][0])
@@ -373,6 +415,11 @@ rule markduplicates:
metrics=c.patterns['markduplicates']['metrics']
log:
c.patterns['markduplicates']['bam'] + '.log'
+ threads: 1
+ resources:
+ mem_mb=1024 * 32,
+ runtime=autobump(120),
+ disk_mb=1024 *100
params:
# NOTE: Be careful with the memory here; make sure you have enough
# and/or it matches the resources you're requesting in the cluster
@@ -408,6 +455,11 @@ rule merge_techreps:
metrics=c.patterns['merged_techreps'] + '.metrics'
log:
c.patterns['merged_techreps'] + '.log'
+ threads: 1
+ resources:
+ mem_mb=1024 * 32,
+ runtime=autobump(120),
+ disk_mb=1024 *100
params:
# NOTE: Be careful with the memory here; make sure you have enough
# and/or it matches the resources you're requesting in the cluster
@@ -426,6 +478,10 @@ if c.is_paired:
metrics=c.patterns['collectinsertsizemetrics']['metrics']
log:
c.patterns['collectinsertsizemetrics']['metrics'] + '.log'
+ threads: 1
+ resources:
+ mem_mb=1024 * 32,
+ runtime=autobump(120),
params:
java_args='-Xmx20g'
# java_args='-Xmx2g' # [TEST SETTINGS -1]
@@ -451,6 +507,10 @@ rule bigwig:
c.patterns['bigwig']
log:
c.patterns['bigwig'] + '.log'
+ threads: 1
+ resources:
+ mem_mb=1024 * 16,
+ runtime=autobump(120)
shell:
'bamCoverage '
'--bam {input.bam} '
@@ -484,6 +544,10 @@ rule fingerprint:
metrics=c.patterns['fingerprint']['metrics']
threads: 8
log: c.patterns['fingerprint']['metrics'] + '.log'
+ threads: 1
+ resources:
+ mem_mb=1024 * 32,
+ runtime=autobump(120)
run:
if len(input.control) == 0:
jsdsample_arg = ""
@@ -529,6 +593,9 @@ rule sicer:
bed=c.patterns['peaks']['sicer']
log:
c.patterns['peaks']['sicer'] + '.log'
+ resources:
+ mem_mb=1024 * 16,
+ runtime=autobump(120)
params:
block=lambda wc: chipseq.block_for_run(config, wc.sicer_run, 'sicer')
wrapper:
@@ -552,6 +619,9 @@ rule macs2:
chromsizes=refdict[c.organism][config['aligner']['tag']]['chromsizes'],
output:
bed=c.patterns['peaks']['macs2']
+ resources:
+ mem_mb=1024 * 16,
+ runtime=autobump(120)
log:
c.patterns['peaks']['macs2'] + '.log'
params:
@@ -583,6 +653,9 @@ rule spp:
rdata=c.patterns['peaks']['spp'] + '.RData'
log:
c.patterns['peaks']['spp'] + '.log'
+ resources:
+ mem_mb=1024 * 16,
+ runtime=autobump(120)
params:
block=lambda wc: chipseq.block_for_run(config, wc.spp_run, 'spp'),
keep_tempfiles=False,
@@ -604,6 +677,9 @@ rule bed_to_bigbed:
bed='{prefix}.bed',
chromsizes=refdict[c.organism][config['aligner']['tag']]['chromsizes']
output: '{prefix}.bigbed'
+ resources:
+ mem_mb=1024 * 2,
+ runtime=autobump(120)
log: '{prefix}.bigbed.log'
run:
# Based on the filename, identify the algorithm. Based on the contents,
@@ -652,6 +728,9 @@ rule multibigwigsummary:
npz=c.targets['multibigwigsummary']['npz'],
tab=c.targets['multibigwigsummary']['tab']
threads: 16
+ resources:
+ mem_mb=1024 * 16,
+ runtime=autobump(120)
run:
# from the input files, figure out the sample name.
labels = ' '.join([i.split('/')[-2] for i in input])
@@ -675,6 +754,9 @@ rule plotcorrelation:
output:
heatmap=c.targets['plotcorrelation']['heatmap'],
tab=c.targets['plotcorrelation']['tab']
+ resources:
+ mem_mb=1024 * 2,
+ runtime=autobump(120)
shell:
'plotCorrelation '
'--corData {input} '
@@ -705,6 +787,9 @@ if 'merged_bigwigs' in config:
chromsizes=refdict[c.organism][config['aligner']['tag']]['chromsizes'],
output:
c.patterns['merged_bigwig']
+ resources:
+ mem_mb=1024 * 16,
+ runtime=autobump(120)
log:
c.patterns['merged_bigwig'] + '.log'
script:
@@ -719,6 +804,9 @@ rule idxstats:
bai=c.patterns['markduplicates']['bam'] + '.bai'
output:
txt=c.patterns['samtools']['idxstats']
+ resources:
+ mem_mb=1024 * 16,
+ runtime=autobump(120)
log:
c.patterns['samtools']['idxstats'] + '.log'
run:
From 12935fb312b61dc5c02fa86ee044e4e261071f20 Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Thu, 23 Feb 2023 15:51:40 -0500
Subject: [PATCH 55/91] fix input.control in fingerprint
---
workflows/chipseq/Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/workflows/chipseq/Snakefile b/workflows/chipseq/Snakefile
index 18a9bb27..1ccdee16 100644
--- a/workflows/chipseq/Snakefile
+++ b/workflows/chipseq/Snakefile
@@ -552,7 +552,7 @@ rule fingerprint:
if len(input.control) == 0:
jsdsample_arg = ""
else:
- jsdsample_arg = '--JSDsample {input.control}'
+ jsdsample_arg = '--JSDsample ' + str(input.control)
shell(
'plotFingerprint ' '--bamfiles {input.bams} '
'-p {threads} '
From 2fcbea5877c17cd82d03767514c6b5470bd3c183 Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Fri, 24 Feb 2023 12:35:07 -0500
Subject: [PATCH 56/91] set --restart-times to 3
---
include/WRAPPER_SLURM | 1 +
1 file changed, 1 insertion(+)
diff --git a/include/WRAPPER_SLURM b/include/WRAPPER_SLURM
index e598572c..393a12fd 100755
--- a/include/WRAPPER_SLURM
+++ b/include/WRAPPER_SLURM
@@ -29,6 +29,7 @@ fi
-p \
--directory $PWD \
-k \
+ --restart-times 3 \
--rerun-incomplete \
--jobname "s.{rulename}.{jobid}.sh" \
-j 999 \
From f29ae61ef1588fd8c06cfb15764b29bd853f0e4f Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Fri, 24 Feb 2023 12:37:05 -0500
Subject: [PATCH 57/91] autobump mem_mb for fastq_dump
---
workflows/rnaseq/Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/workflows/rnaseq/Snakefile b/workflows/rnaseq/Snakefile
index cbef1644..fa41b43a 100644
--- a/workflows/rnaseq/Snakefile
+++ b/workflows/rnaseq/Snakefile
@@ -138,7 +138,7 @@ if 'Run' in c.sampletable.columns and sum(c.sampletable['Run'].str.startswith('S
sampletable=_st,
# limit = 100000, # [TEST SETTINGS]
resources:
- mem_mb=1024,
+ mem_mb=autobump(1024),
runtime=autobump(120)
conda:
'../../wrappers/wrappers/fastq-dump/environment.yaml'
From 62bf67fa6e16d4901579c817f06a99a5e1a90348 Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Mon, 6 Mar 2023 11:20:44 -0500
Subject: [PATCH 58/91] fix volcano plots not showing before barplot
---
lib/lcdbwf/R/plotting.R | 18 ++++++++++++------
lib/lcdbwf/R/results.R | 2 +-
2 files changed, 13 insertions(+), 7 deletions(-)
diff --git a/lib/lcdbwf/R/plotting.R b/lib/lcdbwf/R/plotting.R
index 216871ec..c848f0d9 100644
--- a/lib/lcdbwf/R/plotting.R
+++ b/lib/lcdbwf/R/plotting.R
@@ -340,7 +340,7 @@ counts.plot <- function(df, rank.nb=NULL, no.aes=FALSE, facet='label') {
#' Plot a histogram of raw pvals
#'
-#' This is right out of the DESeq2 vignette, from the section about independent
+#' This is edited from the DESeq2 vignette, from the section about independent
#' filtering. The resulting histogram indicates pvals for those genes kept and
#' removed before multiple testing adjustment.
#'
@@ -352,11 +352,17 @@ pval_hist <- function(res){
h1 <- hist(res$pvalue[!use], breaks=0:50/50, plot=FALSE)
h2 <- hist(res$pvalue[use], breaks=0:50/50, plot=FALSE)
colori <- c(`counts too low`='khaki', `pass`="powderblue")
- barplot(height = rbind(h1$counts, h2$counts), beside = FALSE,
- col = colori, space = 0, main = "", ylab="frequency")
- text(x = c(0, length(h1$counts)), y = 0, label = paste(c(0,1)),
- adj = c(0.5,1.7), xpd=NA)
- legend("topright", fill=rev(colori), legend=rev(names(colori)))
+ df <- rbind(data.frame(x=h1$mids, counts=h1$counts, label='counts too low'),
+ data.frame(x=h2$mids, counts=h2$counts, label='pass')
+ )
+ plt <- ggplot2::ggplot(df, aes(x=x, y=counts, fill=label)) +
+ geom_bar(stat = 'identity', color='gray20') +
+ theme_classic() +
+ scale_fill_manual(values=c("#EBE379", "#A3DAE0")) +
+ xlab('p-value') +
+ ylab('frequency') +
+ theme(legend.position = c(0.8, 0.8))
+ return(plt)
}
#' Barplot of size factors by sample
diff --git a/lib/lcdbwf/R/results.R b/lib/lcdbwf/R/results.R
index d84ecd4c..b1cec3aa 100644
--- a/lib/lcdbwf/R/results.R
+++ b/lib/lcdbwf/R/results.R
@@ -56,7 +56,7 @@ build_results_tabs <- function(res_list, dds_list, config, text){
lcdbwf:::mdcat('### P-value distribution')
lcdbwf:::folded_markdown(text$results_plots$pval_hist, "Help")
- lcdbwf:::pval_hist(res_i)
+ print(lcdbwf:::pval_hist(res_i))
if (config$toggle$results_diagnostics){
lcdbwf:::results_diagnostics(res=res_i, dds=res_list[[name]]$dds, name=name, config=config, text=text)
From 651d4e2fb28b6e728b7fd2f78bc7371ee8bc0454 Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Mon, 6 Mar 2023 11:21:44 -0500
Subject: [PATCH 59/91] allow skipping orgDb
---
lib/lcdbwf/R/annotations.R | 52 +++++++++++++++++++++++---------------
1 file changed, 32 insertions(+), 20 deletions(-)
diff --git a/lib/lcdbwf/R/annotations.R b/lib/lcdbwf/R/annotations.R
index 473c4b95..d1a40b7d 100644
--- a/lib/lcdbwf/R/annotations.R
+++ b/lib/lcdbwf/R/annotations.R
@@ -119,10 +119,11 @@ get_annotation_db <- function(config, dbtype, genus_species=NULL, orgdb_key_over
#'
#' @param res_list List of DESeqResults objects
#' @param config Full config object, at least containing config$orgdb
+#' @param use_orgdb Boolean to use or bypass orgDb extra columns
#'
#' @return List of same results objects, but each one with additional columns
#' attached as specified in the config
-attach_extra <- function(res_list, config, force_intersect){
+attach_extra <- function(res_list, config, force_intersect, use_orgdb=TRUE){
if (missing(force_intersect)) force_intersect <- config$main$force_intersect
if (is.null(force_intersect)) force_intersect <- FALSE
@@ -149,28 +150,39 @@ attach_extra <- function(res_list, config, force_intersect){
keys <- rownames(res_list[[1]]$res)
- orgdb <- lcdbwf:::get_annotation_db(config, dbtype="OrgDb")
+ if (use_orgdb == TRUE) {
+ orgdb <- lcdbwf:::get_annotation_db(config, dbtype="OrgDb")
- # Create a dataframe mapping gene IDs to the various configured columns
- lookups <- list()
- for (col in config$annotation$orgdb_columns){
- lookups[[col]] <- mapIds(orgdb, keys=keys, column=col, keytype=config$annotation$keytype, multiVal='first')
- if (col %in% config$annotation$fill){
- lookups[[col]] <- ifelse(is.na(lookups[[col]]), keys, lookups[[col]])
- }
- }
- lookups <- data.frame(lookups)
-
- # Use that dataframe to attach additional columns to each results object
- for (name in names(res_list)){
- res <- res_list[[name]]$res
- orig_colnames <- colnames(res)
+ # Create a dataframe mapping gene IDs to the various configured columns
+ lookups <- list()
for (col in config$annotation$orgdb_columns){
- res[[col]] <- lookups[[col]]
+ lookups[[col]] <- mapIds(orgdb, keys=keys, column=col, keytype=config$annotation$keytype, multiVal='first')
+ if (col %in% config$annotation$fill){
+ lookups[[col]] <- ifelse(is.na(lookups[[col]]), keys, lookups[[col]])
+ }
+ }
+ lookups <- data.frame(lookups)
+
+ # Use that dataframe to attach additional columns to each results object
+ for (name in names(res_list)){
+ res <- res_list[[name]]$res
+ orig_colnames <- colnames(res)
+ for (col in config$annotation$orgdb_columns){
+ res[[col]] <- lookups[[col]]
+ }
+ res$gene <- rownames(res)
+ res <- res[, c('gene', config$annotation$orgdb_columns, orig_colnames)]
+ res_list[[name]]$res <- res
+ }
+ } else {
+ # attach the genes as SYMBOLs in absence of OrgDb data
+ for (name in names(res_list)){
+ res <- res_list[[name]]$res
+ res$gene <- rownames(res)
+ res$SYMBOL <- rownames(res)
+ res_list[[name]]$res <- res
}
- res$gene <- rownames(res)
- res <- res[, c('gene', config$annotation$orgdb_columns, orig_colnames)]
- res_list[[name]]$res <- res
}
+
return(res_list)
}
From 09e1e2f3ac00a945d6200932c01b5e579c6413d8 Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Tue, 7 Mar 2023 14:32:42 -0500
Subject: [PATCH 60/91] use :::
---
.../downstream/functional-enrichment.Rmd | 32 +++++++++----------
1 file changed, 16 insertions(+), 16 deletions(-)
diff --git a/workflows/rnaseq/downstream/functional-enrichment.Rmd b/workflows/rnaseq/downstream/functional-enrichment.Rmd
index 17df5b9b..f0626f15 100644
--- a/workflows/rnaseq/downstream/functional-enrichment.Rmd
+++ b/workflows/rnaseq/downstream/functional-enrichment.Rmd
@@ -33,7 +33,7 @@ a particular annotation category.
devtools::document('../../../lib/lcdbwf')
devtools::load_all('../../../lib/lcdbwf')
-config <- lcdbwf::load_config('config.yaml')
+config <- lcdbwf:::load_config('config.yaml')
```
```{r load, cache=TRUE, cache.extra=file.info('combined.Rds')$mtime}
@@ -45,8 +45,8 @@ dds_list <- obj$dds_list
```{r functional_enrichment_prep, cache=TRUE, config=config$annotation$keytype, eval=config$toggle$functional_enrichment, dependson='load'}
# We assume that keys are unique across all term2gene_lists.
-term2gene_list <- lcdbwf::get_go_term2gene(config)
-term2name <- lcdbwf::get_go_descriptions()
+term2gene_list <- lcdbwf:::get_go_term2gene(config)
+term2name <- lcdbwf:::get_go_descriptions()
# We need to assign each key to its respective term2name dataframe (or NULL if
# none)
@@ -57,9 +57,9 @@ ontology_list <- c(term2gene_list)
# This can take up a lot of memory on CI/CD, so we only do this if not doing
# a test.
if (!config$toggle$test){
- msigdb_df <- lcdbwf::get_msigdb_df(config)
- msigdb_term2gene_list <- lcdbwf::get_msigdb_term2gene_list(msigdb_df)
- msigdb_term2name <- lcdbwf::get_msigdb_term2name(msigdb_df)
+ msigdb_df <- lcdbwf:::get_msigdb_df(config)
+ msigdb_term2gene_list <- lcdbwf:::get_msigdb_term2gene_list(msigdb_df)
+ msigdb_term2name <- lcdbwf:::get_msigdb_term2name(msigdb_df)
ontology_term2name_mapping <- c(ontology_term2name_mapping, lapply(msigdb_term2gene_list, function(x) NULL))
ontology_list <- c(ontology_list, msigdb_term2gene_list)
}
@@ -78,7 +78,7 @@ for (name in names(res_list)){
for (ont in names(config$functional_enrichment$ontologies)){
term2gene <- ontology_list[[ont]]
term2name <- ontology_term2name_mapping[[ont]]
- enrich_res <- lcdbwf::run_enrichment(
+ enrich_res <- lcdbwf:::run_enrichment(
res_list[[name]],
direction=direction,
TERM2GENE=term2gene,
@@ -99,13 +99,13 @@ for (name in names(res_list)){
```{r functional_enrichment_plots}
# Interestingly, it's the *caching* that causes this to hang for a loooong time.
-dotplot_list <- lcdbwf::enrich_list_lapply(all_enrich, dotplots, config=config, send_names=TRUE)
-emapplot_list <- lcdbwf::enrich_list_lapply(all_enrich, emapplots, config=config, send_names=TRUE)
-cnetplot_list <- lcdbwf::enrich_list_lapply(all_enrich, cnetplots, config=config, send_names=TRUE)
+dotplot_list <- lcdbwf:::enrich_list_lapply(all_enrich, dotplots, config=config, send_names=TRUE)
+emapplot_list <- lcdbwf:::enrich_list_lapply(all_enrich, emapplots, config=config, send_names=TRUE)
+cnetplot_list <- lcdbwf:::enrich_list_lapply(all_enrich, cnetplots, config=config, send_names=TRUE)
```
```{r, results='asis'}
-lcdbwf::mdcat("There are many different databases that annotate genes into sets.",
+lcdbwf:::mdcat("There are many different databases that annotate genes into sets.",
"The following sets are used here:")
knitr::kable(config$functional_enrichment$ontologies %>% as.data.frame %>% t())
@@ -120,19 +120,19 @@ for (name in names(res_list)){
for (direction in config$functional_enrichment$directions){
mdcat("### ", direction, "{.tabset}")
if (length(all_enrich[[name]][[direction]]) == 0){
- lcdbwf::mdcat("Too few genes differentially expressed.")
+ lcdbwf:::mdcat("Too few genes differentially expressed.")
next
}
for (ont in names(all_enrich[[name]][[direction]])){
- lcdbwf::mdcat("#### ", ont, "{.tabset}")
+ lcdbwf:::mdcat("#### ", ont, "{.tabset}")
- lcdbwf::mdcat("##### dotplot")
+ lcdbwf:::mdcat("##### dotplot")
print(dotplot_list[[name]][[direction]][[ont]])
- lcdbwf::mdcat("##### emapplot")
+ lcdbwf:::mdcat("##### emapplot")
print(emapplot_list[[name]][[direction]][[ont]])
- lcdbwf::mdcat("##### cnetplot")
+ lcdbwf:::mdcat("##### cnetplot")
print(cnetplot_list[[name]][[direction]][[ont]])
}
}
From b1c81de170f9c0159ea0d89d43fd3dd426f34372 Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Tue, 7 Mar 2023 14:36:10 -0500
Subject: [PATCH 61/91] modify gene pattern to be stand-alone Rmd
---
workflows/rnaseq/downstream/gene-patterns.Rmd | 107 ++++++++++++++++--
1 file changed, 100 insertions(+), 7 deletions(-)
diff --git a/workflows/rnaseq/downstream/gene-patterns.Rmd b/workflows/rnaseq/downstream/gene-patterns.Rmd
index 56d514c7..e2bf94e0 100644
--- a/workflows/rnaseq/downstream/gene-patterns.Rmd
+++ b/workflows/rnaseq/downstream/gene-patterns.Rmd
@@ -1,3 +1,45 @@
+---
+title: Gene pattern analysis
+output:
+ html_document:
+ code_folding: hide
+ toc: true
+ toc_float: true
+ toc_depth: 3
+---
+
+```{r global_options, include=FALSE}
+# Sets up global options for rendering RMarkdown into HTML.
+knitr::opts_chunk$set(
+ warning=FALSE,
+ message=FALSE
+)
+```
+
+```{r}
+library(dplyr)
+library(tidyr)
+library(clusterProfiler)
+library(DESeq2)
+library(DEGreport)
+```
+
+```{r load_helpers}
+# Load the lcdbwf R package, which is stored locally.
+# This package has many custom functions used throughout this document.
+devtools::document('../../../lib/lcdbwf')
+devtools::load_all('../../../lib/lcdbwf')
+
+config <- lcdbwf:::load_config('config.yaml')
+```
+
+```{r load, cache=TRUE, cache.extra=file.info('combined.Rds')$mtime}
+obj <- readRDS('combined.Rds')
+res.list <- obj$res_list
+dds.list <- obj$dds_list
+```
+
+
# Gene patterns {.tabset}
We can roughly group genes into expression patterns. This uses the [DEGreport
@@ -55,17 +97,23 @@ low.minc <- 1
more, they are merged together
- Clusters with fewer than `r minc` genes are not shown.
+Gene pattern for changed genes in individual contrasts are also indicated below.
+
```{r finalclusters, fig.width=12, results='asis', cache=TRUE, dependson='selections'}
# Run the clustering, identify patterns, and generate plots.
# Docs: https://lcdb.github.io/lcdb-wf/rnaseq-rmd.html#finalclusters
# NOTE: which genes to cluster?------------------------------------------------
# By default, we get all the changed genes, but you may want only the up or
# down genes.
-ll <- lapply(res.list, function (x) get.sig(x[['res']], 'changed'))
+ll <- lapply(res.list, function (x) lcdbwf:::get_sig(x[['res']], 'changed'))
# Filter out results where there were zero genes detected.
ll <- ll[lapply(ll, length) > 0]
+# get the list of all changed in any contrast
+all.changed <- list('union_all_contrasts' = unlist(ll) %>% unique())
+ll <- c(all.changed, ll)
+
add.cluster.id <- function(clusters, res, label){
# Merges the degPattern cluster IDs `cluster` with DESeqresults `res`
# `label` will be used to create a cluster column with a unique column name
@@ -79,9 +127,16 @@ add.cluster.id <- function(clusters, res, label){
return(res)
}
+# n.list will store all the clusters to later add the cluster ID to res.list
+n.list <- list()
+
for (name in names(ll)){
# Print a nice Markdown header
- mdcat('## ', res.list[[name]][['label']])
+ if (name == 'union_all_contrasts') {
+ mdcat('## ', name)
+ } else {
+ mdcat('## ', res.list[[name]][['label']])
+ }
genes <- ll[[name]]
@@ -98,15 +153,23 @@ for (name in names(ll)){
}
# Extract the normalized counts for these genes
- vsd.i <- varianceStabilizingTransformation(dds.list[[ res.list[[name]][['dds']] ]], blind=TRUE)
+ if (name == 'union_all_contrasts') {
+ vsd.i <- varianceStabilizingTransformation(dds.list[[ 1 ]], blind=TRUE)
+ } else {
+ vsd.i <- varianceStabilizingTransformation(dds.list[[ res.list[[name]][['dds']] ]], blind=TRUE)
+ }
idx <- rownames(vsd.i) %in% genes
ma <- assay(vsd.i)[idx,]
# Remove genes with identical normalized counts across all samples
ma <- ma[apply(as.data.frame(ma), 1, n_distinct) > 1, ]
- colData.i <- colData(dds.list[[ res.list[[name]][['dds']] ]])
- colData.i <- colData.i[,!(colnames(colData.i) %in% exclude.for.printing)]
+ if (name == 'union_all_contrasts') {
+ colData.i <- colData(dds.list[[ 1 ]])
+ } else {
+ colData.i <- colData(dds.list[[ res.list[[name]][['dds']] ]])
+ }
+ #colData.i <- colData.i[,!(colnames(colData.i) %in% exclude.for.printing)]
# Sometimes, if there are limited clusters, degPattern fails. The solution
@@ -151,6 +214,7 @@ for (name in names(ll)){
)
)
+ n.list[[name]] <- n2
# In the final_clusters directory, this creates files containing lists of
# the genes in each cluster, and adds a link to the Markdown.
@@ -167,8 +231,37 @@ for (name in names(ll)){
dev.copy(pdf, file=pdf.file)
dev.off()
mdcat('- [', pdf.file, '](', pdf.file, '), PDF')
+}
+```
- # merge the degPattern cluster IDs with res.list
- res.list[[name]][['res']] <- add.cluster.id(clusters=n2, res=res.list[[name]][['res']], label=name)
+```{r add_cluster_id_res}
+# merge the degPattern cluster IDs with res.list
+for (name in names(res.list)) {
+ for (llname in names(ll)) {
+ res.list[[name]][['res']] <- add.cluster.id(clusters=n.list[[llname]],
+ res=res.list[[name]][['res']],
+ label=llname)
+ }
}
```
+
+
+
+# Exported results
+
+```{r excel, results='asis'}
+lcdbwf:::exported_excel(res.list, dds.list, file='final_clusters/consolidated_results.xlsx')
+```
+
+Here is a single Excel file with one worksheet for each contrast:
+[final_clusters/consolidated_results.xlsx](final_clusters/consolidated_results.xlsx)
+
+Alternatively, the files below are TSVs that can be opened in Excel or used
+progammatically with downstream tools:
+
+```{r write_output, results='asis'}
+# Write out files for full and each selection, and create a link to them in the
+# HTML generated by this RMarkdown.
+tbl <- lcdbwf:::exported_tsvs(res.list, directory='final_clusters')
+knitr::kable(tbl, row.names=FALSE)
+```
From 6b0ceae65361717b71ad9ce01bd35dd9f8dcc454 Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Fri, 10 Mar 2023 13:23:16 -0500
Subject: [PATCH 62/91] add R plotting function for scatterplot of 2 contrasts
LFCs color-coded by padj
---
lib/lcdbwf/R/plotting.R | 77 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 77 insertions(+)
diff --git a/lib/lcdbwf/R/plotting.R b/lib/lcdbwf/R/plotting.R
index c848f0d9..c850b9dc 100644
--- a/lib/lcdbwf/R/plotting.R
+++ b/lib/lcdbwf/R/plotting.R
@@ -418,3 +418,80 @@ plotSparsity2 <- function(dds){
}
+
+
+#' Plot a scatterplot of two contrasts' LFCs, color-coded by significance
+#'
+#' This is edited from the DESeq2 vignette, from the section about independent
+#' filtering. The resulting histogram indicates pvals for those genes kept and
+#' removed before multiple testing adjustment.
+#'
+#' @param res_i DESeq2 results object
+#' @param res_j second DESeq2 results object
+#' @param padj.thr float, p.adj threshold
+#' @param name.col string, gene name column to merge the 2 results, also used for labelling plots
+#' @param label_i, label_j string, label for res_i and res_j
+#' @param return.values boolean, whether to return the ggplot object (FALSE) or the dataframe (TRUE)
+#' @param' color.palette list of string, colors to use for significance categories 'Both - same LFC sign',
+#' 'Both - opposite LFC sign 'None', label_i, label_j
+
+#' @return Either returns a ggplot object of the scatterplot, or the corresponding dataframe if return.values=TRUE
+
+lfc_scatter <- function(res_i, res_j, padj.thr=0.1, name.col='SYMBOL', label_i=NULL, label_j=NULL,
+ return.values=FALSE, color.palette=c('#FF3333', "#FF6699", '#999999', '#66CCCC', '#0072B2')) {
+ # colors from color-blind palette red pink grey cyan blue
+ # check whether the genes match in res_i and res_j, emits a warning if not
+ diff.genes <- c(setdiff(rownames(res_i), rownames(res_j)),
+ setdiff(rownames(res_j), rownames(res_i))) %>%
+ unlist() %>%
+ unique()
+ if( length(diff.genes) > 0 ) {
+ warning(paste0(length(diff.genes),
+ ' genes were discarded because found in one res but not the other'))
+ }
+
+ # use generic labels if not provided
+ if (is.null(label_i)) {
+ label_i <- 'LFCs contrast 1'
+ }
+ if (is.null(label_j)) {
+ label_j <- 'LFCs contrast 2'
+ }
+
+ # join results into dataframe
+ cols.sub <- c('log2FoldChange', 'padj', name.col)
+ df <- merge(as.data.frame(res_i)[cols.sub],
+ as.data.frame(res_j)[cols.sub],
+ by= name.col)
+ # add significance column
+ df <- df %>%
+ mutate('Significance' = case_when(
+ (padj.x <= padj.thr) & (padj.y <= padj.thr) & (log2FoldChange.x * log2FoldChange.y >= 0) ~ 'Both - same LFC sign',
+ (padj.x <= padj.thr) & (padj.y <= padj.thr) & (log2FoldChange.x * log2FoldChange.y < 0) ~ 'Both - opposite LFC sign',
+ (padj.x <= padj.thr) ~ label_i,
+ (padj.y <= padj.thr) ~ label_j,
+ TRUE ~ 'None'))
+
+ # if return.values, return the dataframe now, no need to generate the plot
+ if (return.values == TRUE) {
+ return(df)
+ }
+
+ # Significance as factor, to reorder in the graph
+ df[['Significance']] <- factor(df[['Significance']], levels=c('None', label_j, label_i, 'Both - opposite LFC sign', 'Both - same LFC sign'))
+
+ names(color.palette) <- c('Both - same LFC sign', 'Both - opposite LFC sign', 'None', label_i, label_j)
+
+ p <- ggplot(df %>% arrange(Significance), aes_string(x='log2FoldChange.x', y='log2FoldChange.y',
+ color='Significance', label=name.col)) +
+ geom_point(size=1) +
+ theme_bw() +
+ scale_color_manual(values=color.palette) +
+ geom_abline(color="#333333", linetype="dashed", size=0.5, alpha=0.7) +
+ geom_hline(yintercept=0, color="#333333", linetype="dashed", size=0.5, alpha=0.7) +
+ geom_vline(xintercept=0, color="#333333", linetype="dashed", size=0.5, alpha=0.7) +
+ xlab(label_i) +
+ ylab(label_j)
+
+ return(p)
+}
From ad2b6e045fcdc025df008a5fa281d7dfc65fbe17 Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Wed, 29 Mar 2023 13:27:32 -0400
Subject: [PATCH 63/91] make lcdb-wf snakemake profile name consistent with
snakemake
---
include/WRAPPER_SLURM | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/include/WRAPPER_SLURM b/include/WRAPPER_SLURM
index 393a12fd..841058f4 100755
--- a/include/WRAPPER_SLURM
+++ b/include/WRAPPER_SLURM
@@ -8,7 +8,7 @@
if [[ ! -e logs ]]; then mkdir -p logs; fi
# use SNAKEMAKE_PROFILE if one is set in the environment variables
-if [ -z "$LCDBWF_SNAKE_PROFILE" ]; then
+if [ -z "$LCDBWF_SNAKEMAKE_PROFILE" ]; then
if [ -z "$SNAKEMAKE_PROFILE" ]; then
# no snakemake profile found
PROFILE_CMD=""
@@ -19,8 +19,8 @@ if [ -z "$LCDBWF_SNAKE_PROFILE" ]; then
PROFILE_CMD="--profile $SNAKEMAKE_PROFILE"
fi
else
-# LCDBWF_SNAKE_PROFILE found, this takes priority if both profile variables are set
-PROFILE_CMD="--profile $LCDBWF_SNAKE_PROFILE"
+# LCDBWF_SNAKEMAKE_PROFILE found, this takes priority if both profile variables are set
+PROFILE_CMD="--profile $LCDBWF_SNAKEMAKE_PROFILE"
fi
# Run snakemake
From e72a291930203ca53e4789ecd3e980498f1a59a6 Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Wed, 29 Mar 2023 13:28:18 -0400
Subject: [PATCH 64/91] fix fastq-dump autobump
---
workflows/rnaseq/Snakefile | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/workflows/rnaseq/Snakefile b/workflows/rnaseq/Snakefile
index fa41b43a..2798827f 100644
--- a/workflows/rnaseq/Snakefile
+++ b/workflows/rnaseq/Snakefile
@@ -138,7 +138,8 @@ if 'Run' in c.sampletable.columns and sum(c.sampletable['Run'].str.startswith('S
sampletable=_st,
# limit = 100000, # [TEST SETTINGS]
resources:
- mem_mb=autobump(1024),
+ mem_mb=1024,
+ disk_mb=autobump(1024),
runtime=autobump(120)
conda:
'../../wrappers/wrappers/fastq-dump/environment.yaml'
From 7d2be46dd48f056a853f73e28b150e8d4a4bed05 Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Thu, 30 Mar 2023 06:11:43 -0400
Subject: [PATCH 65/91] update env requirements to latest compatible versions
---
env-r.yml | 770 ++++++++++++++++++++++++++++--------------------------
env.yml | 446 ++++++++++++++++---------------
2 files changed, 631 insertions(+), 585 deletions(-)
diff --git a/env-r.yml b/env-r.yml
index 4b30a89a..a23ff911 100644
--- a/env-r.yml
+++ b/env-r.yml
@@ -1,387 +1,403 @@
-name: null
channels:
- conda-forge
- bioconda
dependencies:
- - _libgcc_mutex=0.1=conda_forge
+ - _libgcc_mutex=0.1
- _openmp_mutex=4.5=2_gnu
- - _r-mutex=1.0.1=anacondar_1
- - binutils_impl_linux-64=2.39=h6ceecb4_0
- - bioconductor-all=1.32.0=r40hdfd78af_1
- - bioconductor-annotate=1.68.0=r40hdfd78af_1
- - bioconductor-annotationdbi=1.52.0=r40hdfd78af_1
- - bioconductor-annotationhub=2.22.0=r40hdfd78af_1
- - bioconductor-apeglm=1.12.0=r40h399db7b_1
- - bioconductor-biobase=2.50.0=r40hd029910_1
- - bioconductor-biocfilecache=1.14.0=r40hdfd78af_1
- - bioconductor-biocgenerics=0.36.0=r40hdfd78af_1
- - bioconductor-biocparallel=1.24.1=r40h399db7b_0
- - bioconductor-biocversion=3.12.0=r40hdfd78af_1
- - bioconductor-biomart=2.46.3=r40hdfd78af_0
- - bioconductor-biostrings=2.58.0=r40hd029910_1
- - bioconductor-clusterprofiler=3.18.1=r40hdfd78af_0
- - bioconductor-complexheatmap=2.6.2=r40hdfd78af_1
- - bioconductor-consensusclusterplus=1.54.0=r40hdfd78af_1
- - bioconductor-degreport=1.26.0=r40hdfd78af_1
- - bioconductor-delayedarray=0.16.3=r40hd029910_0
- - bioconductor-deseq2=1.30.1=r40h399db7b_0
- - bioconductor-do.db=2.9=r40hdfd78af_10
- - bioconductor-dose=3.16.0=r40hdfd78af_1
- - bioconductor-dupradar=1.20.0=r40hdfd78af_1
- - bioconductor-edger=3.32.1=r40h399db7b_0
- - bioconductor-enrichplot=1.10.2=r40hdfd78af_0
- - bioconductor-fgsea=1.16.0=r40h399db7b_1
- - bioconductor-genefilter=1.72.1=r40hba52eb8_0
- - bioconductor-geneplotter=1.68.0=r40hdfd78af_1
- - bioconductor-genomeinfodb=1.26.4=r40hdfd78af_0
- - bioconductor-genomeinfodbdata=1.2.4=r40hdfd78af_2
- - bioconductor-genomicalignments=1.26.0=r40hd029910_1
- - bioconductor-genomicfeatures=1.42.2=r40hdfd78af_0
- - bioconductor-genomicranges=1.42.0=r40hd029910_1
- - bioconductor-go.db=3.12.1=r40hdfd78af_1
- - bioconductor-gosemsim=2.16.1=r40h399db7b_0
- - bioconductor-graph=1.68.0=r40hd029910_1
- - bioconductor-graphite=1.36.0=r40hdfd78af_1
- - bioconductor-ihw=1.18.0=r40hdfd78af_1
- - bioconductor-interactivedisplaybase=1.28.0=r40hdfd78af_1
- - bioconductor-iranges=2.24.1=r40hd029910_0
- - bioconductor-limma=3.46.0=r40hd029910_1
- - bioconductor-lpsymphony=1.18.0=r40h399db7b_1
- - bioconductor-matrixgenerics=1.2.1=r40hdfd78af_0
- - bioconductor-qvalue=2.22.0=r40hdfd78af_1
- - bioconductor-reactome.db=1.74.0=r40hdfd78af_1
- - bioconductor-reactomepa=1.34.0=r40hdfd78af_1
- - bioconductor-rhdf5=2.34.0=r40h399db7b_1
- - bioconductor-rhdf5filters=1.2.0=r40h399db7b_1
- - bioconductor-rhdf5lib=1.12.1=r40hd029910_0
- - bioconductor-rhtslib=1.22.0=r40hd029910_1
- - bioconductor-rsamtools=2.6.0=r40h399db7b_1
- - bioconductor-rsubread=2.4.3=r40hd029910_0
- - bioconductor-rtracklayer=1.50.0=r40h7f5ccec_2
- - bioconductor-s4vectors=0.28.1=r40hd029910_0
- - bioconductor-summarizedexperiment=1.20.0=r40hdfd78af_1
- - bioconductor-sva=3.38.0=r40hd029910_1
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- - r-upsetr=1.4.0=r40hc72bb7e_2
- - r-urlchecker=1.0.1=r40hc72bb7e_0
- - r-usethis=2.1.6=r40hc72bb7e_0
- - r-utf8=1.2.2=r40hcfec24a_0
- - r-vctrs=0.4.1=r40h7525677_0
- - r-viridis=0.6.2=r40hc72bb7e_0
- - r-viridislite=0.4.1=r40hc72bb7e_0
- - r-vroom=1.5.7=r40h03ef668_0
- - r-waldo=0.4.0=r40hc72bb7e_0
- - r-webshot=0.5.4=r40hc72bb7e_0
- - r-whisker=0.4=r40hc72bb7e_1
- - r-withr=2.5.0=r40hc72bb7e_0
- - r-xfun=0.33=r40h7525677_0
- - r-xml=3.99_0.10=r40h06615bd_0
- - r-xml2=1.3.3=r40h7525677_1
- - r-xopen=1.0.0=r40hc72bb7e_1003
- - r-xtable=1.8_4=r40hc72bb7e_3
- - r-yaml=2.3.5=r40h06615bd_0
- - r-yulab.utils=0.0.5=r40hc72bb7e_0
- - r-zip=2.2.1=r40h06615bd_0
- - readline=8.1.2=h0f457ee_0
- - sed=4.8=he412f7d_0
- - sysroot_linux-64=2.12=he073ed8_15
- - tk=8.6.12=h27826a3_0
- - tktable=2.10=hb7b940f_3
- - xorg-kbproto=1.0.7=h7f98852_1002
- - xorg-libice=1.0.10=h7f98852_0
- - xorg-libsm=1.2.3=hd9c2040_1000
- - xorg-libx11=1.7.2=h7f98852_0
- - xorg-libxau=1.0.9=h7f98852_0
- - xorg-libxdmcp=1.1.3=h7f98852_0
- - xorg-libxext=1.3.4=h7f98852_1
- - xorg-libxrender=0.9.10=h7f98852_1003
- - xorg-libxt=1.2.1=h7f98852_2
- - xorg-renderproto=0.11.1=h7f98852_1002
- - xorg-xextproto=7.3.0=h7f98852_1002
- - xorg-xproto=7.0.31=h7f98852_1007
- - xz=5.2.6=h166bdaf_0
- - zlib=1.2.13=h166bdaf_4
- - zstd=1.5.2=h6239696_4
-prefix: /home/dalerr/proj/lcdb-wf/env-r
+ - libnghttp2=1.51.0
+ - libnsl=2.0.0
+ - libopenblas=0.3.21
+ - libpng=1.6.39
+ - libsanitizer=12.2.0
+ - libsqlite=3.40.0
+ - libssh2=1.10.0
+ - libstdcxx-devel_linux-64=12.2.0
+ - libstdcxx-ng=12.2.0
+ - libtiff=4.5.0
+ - libuuid=2.38.1
+ - libwebp-base=1.3.0
+ - libxcb=1.13
+ - libxml2=2.10.3
+ - libzlib=1.2.13
+ - make=4.3
+ - ncurses=6.3
+ - oniguruma=6.9.8
+ - openssl=1.1.1t
+ - pandoc=2.19.2
+ - pango=1.50.14
+ - pcre2=10.40
+ - pixman=0.40.0
+ - pthread-stubs=0.4
+ - python=3.11.0
+ - python_abi=3.11=3_cp311
+ - r-ape=5.7_1
+ - r-aplot=0.1.10
+ - r-ashr=2.2_54
+ - r-askpass=1.1
+ - r-assertthat=0.2.1
+ - r-babelgene=22.9
+ - r-backports=1.4.1
+ - r-base=4.2.2
+ - r-base64enc=0.1_3
+ - r-bbmle=1.0.25
+ - r-bdsmatrix=1.3_6
+ - r-bh=1.81.0_1
+ - r-biocmanager=1.30.20
+ - r-bit=4.0.5
+ - r-bit64=4.0.5
+ - r-bitops=1.0_7
+ - r-blob=1.2.4
+ - r-brew=1.0_8
+ - r-brio=1.1.3
+ - r-broom=1.0.4
+ - r-bslib=0.4.2
+ - r-ca=0.71.1
+ - r-cachem=1.0.7
+ - r-callr=3.7.3
+ - r-circlize=0.4.15
+ - r-cli=3.6.1
+ - r-clipr=0.8.0
+ - r-clue=0.3_64
+ - r-cluster=2.1.4
+ - r-coda=0.19_4
+ - r-codetools=0.2_19
+ - r-colorspace=2.1_0
+ - r-commonmark=1.9.0
+ - r-cowplot=1.1.1
+ - r-cpp11=0.4.3
+ - r-crayon=1.5.2
+ - r-credentials=1.3.2
+ - r-crosstalk=1.2.0
+ - r-curl=4.3.3
+ - r-data.table=1.14.8
+ - r-dbi=1.1.3
+ - r-dbplyr=2.3.2
+ - r-dendextend=1.17.1
+ - r-desc=1.4.2
+ - r-devtools=2.4.5
+ - r-diffobj=0.3.5
+ - r-digest=0.6.31
+ - r-doparallel=1.0.17
+ - r-downlit=0.4.2
+ - r-downloader=0.4
+ - r-dplyr=1.1.1
+ - r-dt=0.27
+ - r-egg=0.4.5
+ - r-ellipsis=0.3.2
+ - r-emdbook=1.3.12
+ - r-etrunct=0.1
+ - r-evaluate=0.20
+ - r-fansi=1.0.4
+ - r-farver=2.1.1
+ - r-fastmap=1.1.1
+ - r-fastmatch=1.1_3
+ - r-fdrtool=1.2.17
+ - r-filelock=1.0.2
+ - r-fontawesome=0.5.0
+ - r-forcats=1.0.0
+ - r-foreach=1.5.2
+ - r-formatr=1.14
+ - r-fs=1.6.1
+ - r-futile.logger=1.4.3
+ - r-futile.options=1.0.1
+ - r-gclus=1.3.2
+ - r-generics=0.1.3
+ - r-gert=1.9.2
+ - r-getoptlong=1.0.5
+ - r-ggally=2.1.2
+ - r-ggdendro=0.1.23
+ - r-ggforce=0.4.1
+ - r-ggfun=0.0.9
+ - r-ggnewscale=0.4.8
+ - r-ggplot2=3.4.1
+ - r-ggplotify=0.1.0
+ - r-ggraph=2.1.0
+ - r-ggrepel=0.9.3
+ - r-gh=1.4.0
+ - r-gitcreds=0.1.2
+ - r-globaloptions=0.1.2
+ - r-glue=1.6.2
+ - r-graphlayouts=0.8.4
+ - r-gridextra=2.3
+ - r-gridgraphics=0.5_1
+ - r-gson=0.1.0
+ - r-gtable=0.3.3
+ - r-heatmaply=1.4.2
+ - r-hexbin=1.28.3
+ - r-highr=0.10
+ - r-hms=1.1.3
+ - r-htmltools=0.5.5
+ - r-htmlwidgets=1.6.2
+ - r-httpuv=1.6.9
+ - r-httr=1.4.5
+ - r-httr2=0.2.2
+ - r-igraph=1.4.1
+ - r-ini=0.3.1
+ - r-invgamma=1.1
+ - r-irlba=2.3.5.1
+ - r-isoband=0.2.7
+ - r-iterators=1.0.14
+ - r-jquerylib=0.1.4
+ - r-jsonlite=1.8.4
+ - r-knitr=1.42
+ - r-labeling=0.4.2
+ - r-lambda.r=1.2.4
+ - r-later=1.3.0
+ - r-lattice=0.20_45
+ - r-lazyeval=0.2.2
+ - r-lifecycle=1.0.3
+ - r-locfit=1.5_9.7
+ - r-logging=0.10_108
+ - r-magrittr=2.0.3
+ - r-mass=7.3_58.3
+ - r-matrix=1.5_3
+ - r-matrixstats=0.63.0
+ - r-memoise=2.0.1
+ - r-mgcv=1.8_42
+ - r-mime=0.12
+ - r-miniui=0.1.1.1
+ - r-mixsqp=0.3_48
+ - r-mnormt=2.1.1
+ - r-msigdbr=7.5.1
+ - r-munsell=0.5.0
+ - r-mvtnorm=1.1_3
+ - r-nlme=3.1_162
+ - r-numderiv=2016.8_1.1
+ - r-openssl=2.0.5
+ - r-openxlsx=4.2.5.2
+ - r-patchwork=1.1.2
+ - r-pheatmap=1.0.12
+ - r-pillar=1.9.0
+ - r-pkgbuild=1.4.0
+ - r-pkgconfig=2.0.3
+ - r-pkgdown=2.0.7
+ - r-pkgload=1.3.2
+ - r-plogr=0.2.0
+ - r-plotly=4.10.1
+ - r-plyr=1.8.8
+ - r-png=0.1_8
+ - r-polyclip=1.10_4
+ - r-praise=1.0.0
+ - r-prettyunits=1.1.1
+ - r-processx=3.8.0
+ - r-profvis=0.3.7
+ - r-progress=1.2.2
+ - r-promises=1.2.0.1
+ - r-ps=1.7.3
+ - r-psych=2.3.3
+ - r-purrr=1.0.1
+ - r-qap=0.1_2
+ - r-r6=2.5.1
+ - r-ragg=1.2.5
+ - r-rappdirs=0.3.3
+ - r-rcmdcheck=1.4.0
+ - r-rcolorbrewer=1.1_3
+ - r-rcpp=1.0.10
+ - r-rcpparmadillo=0.11.4.4.0
+ - r-rcppeigen=0.3.3.9.3
+ - r-rcppnumerical=0.5_0
+ - r-rcurl=1.98_1.10
+ - r-readr=2.1.4
+ - r-registry=0.5_1
+ - r-rematch2=2.1.2
+ - r-remotes=2.4.2
+ - r-reshape=0.8.9
+ - r-reshape2=1.4.4
+ - r-restfulr=0.0.15
+ - r-rjson=0.2.21
+ - r-rlang=1.1.0
+ - r-rmarkdown=2.21
+ - r-roxygen2=7.2.3
+ - r-rprojroot=2.0.3
+ - r-rsqlite=2.3.0
+ - r-rstudioapi=0.14
+ - r-rvcheck=0.2.1
+ - r-rversions=2.1.2
+ - r-sass=0.4.5
+ - r-scales=1.2.1
+ - r-scatterpie=0.1.8
+ - r-seriation=1.4.2
+ - r-sessioninfo=1.2.2
+ - r-shadowtext=0.1.2
+ - r-shape=1.4.6
+ - r-shiny=1.7.4
+ - r-slam=0.1_50
+ - r-snow=0.4_4
+ - r-sourcetools=0.1.7_1
+ - r-sparsem=1.81
+ - r-squarem=2021.1
+ - r-stringi=1.7.12
+ - r-stringr=1.5.0
+ - r-survival=3.5_5
+ - r-sys=3.4.1
+ - r-systemfonts=1.0.4
+ - r-testthat=3.1.7
+ - r-textshaping=0.3.6
+ - r-tibble=3.2.1
+ - r-tidygraph=1.2.3
+ - r-tidyr=1.3.0
+ - r-tidyselect=1.2.0
+ - r-tidytree=0.4.2
+ - r-tinytex=0.44
+ - r-tmvnsim=1.0_2
+ - r-truncnorm=1.0_9
+ - r-tsp=1.2_3
+ - r-tweenr=2.0.2
+ - r-tzdb=0.3.0
+ - r-upsetr=1.4.0
+ - r-urlchecker=1.0.1
+ - r-usethis=2.1.6
+ - r-utf8=1.2.3
+ - r-vctrs=0.6.1
+ - r-viridis=0.6.2
+ - r-viridislite=0.4.1
+ - r-vroom=1.6.1
+ - r-waldo=0.4.0
+ - r-webshot=0.5.4
+ - r-whisker=0.4.1
+ - r-withr=2.5.0
+ - r-xfun=0.38
+ - r-xml=3.99_0.14
+ - r-xml2=1.3.3
+ - r-xopen=1.0.0
+ - r-xtable=1.8_4
+ - r-yaml=2.3.7
+ - r-yulab.utils=0.0.6
+ - r-zip=2.2.2
+ - readline=8.2
+ - sed=4.8
+ - sysroot_linux-64=2.12
+ - tk=8.6.12
+ - tktable=2.10
+ - tzdata=2023c
+ - xorg-kbproto=1.0.7
+ - xorg-libice=1.0.10
+ - xorg-libsm=1.2.3
+ - xorg-libx11=1.8.4
+ - xorg-libxau=1.0.9
+ - xorg-libxdmcp=1.1.3
+ - xorg-libxext=1.3.4
+ - xorg-libxrender=0.9.10
+ - xorg-libxt=1.2.1
+ - xorg-renderproto=0.11.1
+ - xorg-xextproto=7.3.0
+ - xorg-xproto=7.0.31
+ - xz=5.2.6
+ - yaml=0.2.5
+ - zlib=1.2.13
+ - zstd=1.5.2
+ - argcomplete=3.0.5
+ - pip=23.0.1
+ - pyyaml=6.0
+ - setuptools=67.6.1
+ - toml=0.10.2
+ - wheel=0.40.0
+ - xmltodict=0.13.0
+ - yq=3.1.1
diff --git a/env.yml b/env.yml
index 66a8bd01..a47dcab5 100644
--- a/env.yml
+++ b/env.yml
@@ -5,302 +5,185 @@ dependencies:
- _libgcc_mutex=0.1
- _openmp_mutex=4.5
- _r-mutex=1.0.1
- - alsa-lib=1.2.3.2
- - amply=0.1.5
- - appdirs=1.4.4
- - argcomplete=2.0.0
- - argh=0.26.2
- - asttokens=2.0.8
+ - alsa-lib=1.2.8
- attr=2.5.1
- - attrs=22.1.0
- - backcall=0.2.0
- backports=1.0
- backports.functools_lru_cache=1.6.4
- bedtools=2.30.0
- - binutils_impl_linux-64=2.39
- - binutils_linux-64=2.39
- - biopython=1.79
- - boost-cpp=1.74.0
+ - binutils_impl_linux-64=2.40
- bowtie=1.3.1
- - bowtie2=2.5.0
+ - bowtie2=2.5.1
- brotli=1.0.9
- brotli-bin=1.0.9
- - brotlipy=0.7.0
- bwidget=1.9.14
- - bx-python=0.9.0
- bzip2=1.0.8
- c-ares=1.18.1
- - ca-certificates=2022.9.24
+ - ca-certificates=2022.12.7
- cairo=1.16.0
- - certifi=2022.9.24
- - cffi=1.15.1
- - charset-normalizer=2.1.1
- - click=8.1.3
- coin-or-cbc=2.10.8
- coin-or-cgl=0.60.6
- coin-or-clp=1.17.7
- coin-or-osi=0.108.7
- coin-or-utils=2.11.6
- coincbc=2.10.8
- - colorama=0.4.6
- - coloredlogs=15.0.1
- - colormath=3.0.0
- - commonmark=0.9.1
- - configargparse=1.5.3
- connection_pool=0.0.3
- - contourpy=1.0.6
- - cryptography=38.0.2
- - curl=7.86.0
- - cutadapt=4.1
- - cycler=0.11.0
- - dataclasses=0.8
- - datrie=0.8.2
+ - curl=7.87.0
- dbus=1.13.6
- - decorator=5.1.1
- - deeptools=3.5.1
- - deeptoolsintervals=0.1.9
- - dnaio=0.9.1
- - docutils=0.19
- - dpath=2.0.6
- - exceptiongroup=1.0.0
- - execnet=1.9.0
- - executing=1.1.1
- expat=2.5.0
- fastq-screen=0.15.2
- - fastqc=0.11.9
+ - fastqc=0.12.1
- fftw=3.3.10
- - filelock=3.8.0
- font-ttf-dejavu-sans-mono=2.37
- font-ttf-inconsolata=3.000
- font-ttf-source-code-pro=2.038
- font-ttf-ubuntu=0.83
- - fontconfig=2.14.1
- - fonts-conda-ecosystem=1
- - fonts-conda-forge=1
- - fonttools=4.38.0
+ - fontconfig=2.14.2
+ - fonts-conda-ecosystem=1=0
+ - fonts-conda-forge=1=0
- freetype=2.12.1
- fribidi=1.0.10
- - future=0.18.2
- - gat=1.3.6
- - gcc_impl_linux-64=10.4.0
- - gcc_linux-64=10.4.0
+ - gcc_impl_linux-64=12.2.0
- gettext=0.21.1
- gffread=0.12.7
- - gffutils=0.11.1
- - gfortran_impl_linux-64=10.4.0
- - gfortran_linux-64=10.4.0
+ - gfortran_impl_linux-64=12.2.0
- giflib=5.2.1
- - gitdb=4.0.9
- - gitpython=3.1.29
- glib=2.74.1
- glib-tools=2.74.1
- graphite2=1.3.13
- gsl=2.7
- - gst-plugins-base=1.18.5
- - gstreamer=1.20.3
- - gxx_impl_linux-64=10.4.0
- - gxx_linux-64=10.4.0
- - harfbuzz=4.2.0
+ - gst-plugins-base=1.21.3
+ - gstreamer=1.21.3
+ - gstreamer-orc=0.4.33
+ - gxx_impl_linux-64=12.2.0
+ - harfbuzz=6.0.0
- hdf5=1.12.1
- hisat2=2.2.1
- - htslib=1.16
- - humanfriendly=10.0
- - icu=69.1
- - idna=3.4
- - importlib-metadata=4.11.4
- - importlib_metadata=4.11.4
- - importlib_resources=5.10.0
- - iniconfig=1.1.1
- - intervalstats=1.01
- - ipython=8.6.0
+ - htslib=1.17
+ - icu=70.1
+ - importlib_resources=5.12.0
+ - intervalstats=1.01=0
- isa-l=2.30.0
- - jack=1.9.18
- - jedi=0.18.1
- - jinja2=3.1.2
+ - jack=1.9.22
- jpeg=9e
- - jsonschema=4.16.0
- - jupyter_core=4.11.1
+ - jupyter_core=5.3.0
- kallisto=0.48.0
- kernel-headers_linux-64=2.6.32
- keyutils=1.6.1
- - kiwisolver=1.4.4
- - krb5=1.19.3
- - lcms2=2.13.1
- - ld_impl_linux-64=2.39
+ - krb5=1.20.1
+ - lame=3.100
+ - lcms2=2.14
+ - ld_impl_linux-64=2.40
- lerc=4.0.0
- libblas=3.9.0
- libbrotlicommon=1.0.9
- libbrotlidec=1.0.9
- libbrotlienc=1.0.9
- - libcap=2.64
+ - libcap=2.66
- libcblas=3.9.0
- - libclang=13.0.1
+ - libclang=15.0.7
+ - libclang13=15.0.7
- libcups=2.3.3
- - libcurl=7.86.0
+ - libcurl=7.87.0
- libdb=6.2.32
- libdeflate=1.13
- libedit=3.1.20191231
- libev=4.33
- libevent=2.1.10
- libffi=3.4.2
- - libflac=1.3.4
- - libgcc-devel_linux-64=10.4.0
+ - libflac=1.4.2
+ - libgcc-devel_linux-64=12.2.0
- libgcc-ng=12.2.0
+ - libgcrypt=1.10.1
- libgd=2.3.3
- libgfortran-ng=12.2.0
- libgfortran5=12.2.0
- libglib=2.74.1
- libgomp=12.2.0
+ - libgpg-error=1.46
+ - libhwloc=2.9.0
- libiconv=1.17
- - libjemalloc=5.2.1
- liblapack=3.9.0
- liblapacke=3.9.0
- - libllvm13=13.0.1
- - libnghttp2=1.47.0
+ - libllvm15=15.0.7
+ - libnghttp2=1.51.0
- libnsl=2.0.0
- libogg=1.3.4
- libopenblas=0.3.21
- libopus=1.3.1
- - libpng=1.6.38
- - libpq=14.5
- - libsanitizer=10.4.0
- - libsndfile=1.0.31
- - libsqlite=3.39.4
+ - libpng=1.6.39
+ - libpq=15.1
+ - libsanitizer=12.2.0
+ - libsndfile=1.2.0
+ - libsqlite=3.40.0
- libssh2=1.10.0
- - libstdcxx-devel_linux-64=10.4.0
+ - libstdcxx-devel_linux-64=12.2.0
- libstdcxx-ng=12.2.0
+ - libsystemd0=252
- libtiff=4.4.0
- - libtool=2.4.6
- - libudev1=251
- - libuuid=2.32.1
+ - libtool=2.4.7
+ - libudev1=253
+ - libuuid=2.38.1
- libvorbis=1.3.7
- libwebp=1.2.4
- libwebp-base=1.2.4
- libxcb=1.13
- - libxkbcommon=1.0.3
- - libxml2=2.9.12
+ - libxkbcommon=1.5.0
+ - libxml2=2.10.3
- libzlib=1.2.13
+ - lz4-c=1.9.4
- lzo=2.10
- - lzstring=1.0.4
- make=4.3
- - markdown=3.4.1
- - markupsafe=2.1.1
- - matplotlib=3.6.0
- - matplotlib-base=3.6.0
- - matplotlib-inline=0.1.6
- - multiqc=1.13
- - munkres=1.1.4
- - mysql-common=8.0.31
+ - matplotlib-base=3.7.1
+ - mpg123=1.31.3
+ - mysql-common=8.0.32
- mysql-connector-c=6.1.11
- - mysql-libs=8.0.31
- - nbformat=5.7.0
+ - mysql-libs=8.0.32
- ncurses=6.3
- - networkx=2.8.7
- - nspr=4.32
- - nss=3.78
- - numpy=1.23.4
- - openjdk=11.0.1
+ - nspr=4.35
+ - nss=3.89
+ - openjdk=17.0.3
- openjpeg=2.5.0
- - openssl=1.1.1q
- - packaging=21.3
- - pandas=1.5.1
- - pandoc=2.19.2
- - pango=1.50.7
- - parso=0.8.3
- - patsy=0.5.3
- - pbzip2=1.1.13
- - pcre2=10.37
+ - openssl=1.1.1t
+ - pandoc=3.1.1
+ - pango=1.50.14
+ - pbzip2=1.1.13=0
+ - pcre2=10.40
- perl=5.32.1
- perl-gd=2.76
- perl-gdgraph=1.54
- perl-gdtextutil=0.86
- - pexpect=4.8.0
- - picard=2.27.4
- - pickleshare=0.7.5
+ - picard=3.0.0
- pigz=2.6
- - pillow=9.2.0
- - pip=22.3
- pixman=0.40.0
- - pkgutil-resolve-name=1.3.10
- - plac=1.3.5
- - plotly=5.11.0
- - pluggy=1.0.0
- preseq=3.2.0
- - prompt-toolkit=3.0.31
- - psutil=5.9.3
+ - prompt_toolkit=3.0.38
- pthread-stubs=0.4
- - ptyprocess=0.7.0
- - pulp=2.6.0
- - pulseaudio=14.0
+ - pulseaudio=16.1
- pure_eval=0.2.2
- - py2bit=0.3.0
- - pybedtools=0.9.0
- - pybigwig=0.3.18
- - pycparser=2.21
- - pyfaidx=0.7.1
- - pygments=2.13.0
- - pyopenssl=22.1.0
- - pyparsing=3.0.9
- - pyqt=5.15.4
- - pyqt5-sip=12.9.0
- - pyrsistent=0.18.1
- - pysam=0.19.1
- - pysocks=1.7.1
- - pytest=7.2.0
- - pytest-xdist=3.0.2
- - python=3.10.6
- - python-dateutil=2.8.2
- - python-fastjsonschema=2.16.2
+ - pyqt=5.15.7
+ - python=3.10.8
+ - python-fastjsonschema=2.16.3
- python-isal=1.1.0
- - python-lzo=1.14
- - python_abi=3.10
- - pytz=2022.5
- - pyvcf3=1.0.3
- - pyyaml=6.0
- - qt-main=5.15.2
- - r-base=4.1.3
- - ratelimiter=1.2.0
- - readline=8.1.2
- - requests=2.28.1
- - reretry=0.11.1
- - rich=12.6.0
- - rich-click=1.5.2
- - rseqc=5.0.1
- - salmon=1.9.0
+ - python_abi=3.10=3_cp310
+ - qt-main=5.15.6
+ - r-base=4.2.2
+ - readline=8.2
+ - salmon=0.8.1=0
- samtools=1.16.1
- - scipy=1.9.3
- - seaborn=0.12.1
- - seaborn-base=0.12.1
+ - seaborn-base=0.12.2
- sed=4.8
- - setuptools=65.5.0
- - simplejson=3.17.6
- - sip=6.5.1
- - six=1.16.0
- - smart_open=6.2.0
- - smmap=3.0.5
- - snakemake-minimal=7.17.1
- - spectra=0.0.11
- - sqlite=3.39.4
+ - smart_open=6.3.0
+ - snakemake-minimal=7.25.0
- sra-tools=2.9.6
- - stack_data=0.5.1
- - star=2.7.10a
- - statsmodels=0.13.2
- - stopit=1.1.2
- - subread=2.0.1
+ - stack_data=0.6.2
+ - star=2.7.10b
+ - subread=2.0.3
- sysroot_linux-64=2.12
- - tabulate=0.9.0
- - tbb=2021.6.0
- - tenacity=8.1.0
+ - tbb=2021.8.0
- tk=8.6.12
- tktable=2.10
- - toml=0.10.2
- - tomli=2.0.1
- - toposort=1.7
- - tornado=6.2
- - trackhub=0.2.4
- - traitlets=5.5.0
- - typing_extensions=4.4.0
- - tzdata=2022f
+ - typing_extensions=4.5.0
+ - tzdata=2023c
- ucsc-bedgraphtobigwig=377
- ucsc-bedsort=377
- ucsc-bedtobigbed=377
@@ -312,27 +195,174 @@ dependencies:
- ucsc-oligomatch=377
- ucsc-twobittofa=377
- ucsc-wigtobigwig=377
- - unicodedata2=15.0.0
- - urllib3=1.26.11
- - wcwidth=0.2.5
- - wheel=0.37.1
- - wrapt=1.14.1
- - xopen=1.6.0
+ - xcb-util=0.4.0
+ - xcb-util-image=0.4.0
+ - xcb-util-keysyms=0.4.0
+ - xcb-util-renderutil=0.3.9
+ - xcb-util-wm=0.4.1
+ - xkeyboard-config=2.38
+ - xorg-fixesproto=5.0
+ - xorg-inputproto=2.3.2
- xorg-kbproto=1.0.7
- xorg-libice=1.0.10
- xorg-libsm=1.2.3
- - xorg-libx11=1.7.2
+ - xorg-libx11=1.8.4
- xorg-libxau=1.0.9
- xorg-libxdmcp=1.1.3
- xorg-libxext=1.3.4
+ - xorg-libxfixes=5.0.3
+ - xorg-libxi=1.7.10
- xorg-libxrender=0.9.10
- xorg-libxt=1.2.1
+ - xorg-libxtst=1.2.3
+ - xorg-recordproto=1.14.2
- xorg-renderproto=0.11.1
- xorg-xextproto=7.3.0
- xorg-xproto=7.0.31
- xz=5.2.6
- yaml=0.2.5
- - yte=1.5.1
- - zipp=3.10.0
- zlib=1.2.13
- zstd=1.5.2
+ - amply=0.1.5
+ - appdirs=1.4.4
+ - argcomplete=3.0.5
+ - argh=0.27.2
+ - asttokens=2.2.1
+ - attrs=22.2.0
+ - backcall=0.2.0
+ - backports.functools_lru_cache=1.6.4
+ - biopython=1.81
+ - brotlipy=0.7.0
+ - bx-python=0.9.0
+ - certifi=2022.12.7
+ - cffi=1.15.1
+ - charset-normalizer=2.1.1
+ - click=8.1.3
+ - colorama=0.4.6
+ - coloredlogs=15.0.1
+ - colormath=3.0.0
+ - configargparse=1.5.3
+ - connection_pool=0.0.3
+ - contourpy=1.0.7
+ - cryptography=39.0.0
+ - cutadapt=4.3
+ - cycler=0.11.0
+ - datrie=0.8.2
+ - decorator=5.1.1
+ - deeptools=3.5.1
+ - deeptoolsintervals=0.1.9
+ - dnaio=0.10.0
+ - docutils=0.19
+ - dpath=2.1.5
+ - exceptiongroup=1.1.1
+ - execnet=1.9.0
+ - executing=1.2.0
+ - python-fastjsonschema=2.16.3
+ - filelock=3.10.7
+ - fonttools=4.39.3
+ - future=0.18.3
+ - gat=1.3.6
+ - gffutils=0.11.1
+ - gitdb=4.0.10
+ - gitpython=3.1.31
+ - humanfriendly=10.0
+ - idna=3.4
+ - importlib-metadata=6.1.0
+ - importlib-resources=5.12.0
+ - iniconfig=2.0.0
+ - ipython=8.11.0
+ - python-isal=1.1.0
+ - jedi=0.18.2
+ - jinja2=3.1.2
+ - jsonschema=4.17.3
+ - jupyter_core=5.3.0
+ - kiwisolver=1.4.4
+ - lzstring=1.0.4
+ - markdown=3.4.3
+ - markdown-it-py=2.2.0
+ - markupsafe=2.1.2
+ - matplotlib=3.7.1
+ - matplotlib-inline=0.1.6
+ - mdurl=0.1.0
+ - multiqc=1.14
+ - munkres=1.1.4
+ - nbformat=5.8.0
+ - networkx=3.0
+ - numpy=1.23.5
+ - packaging=23.0
+ - pandas=1.5.3
+ - parso=0.8.3
+ - patsy=0.5.3
+ - pexpect=4.8.0
+ - pickleshare=0.7.5
+ - pillow=9.2.0
+ - pip=23.0.1
+ - pkgutil-resolve-name=1.3.10
+ - plac=1.3.5
+ - platformdirs=3.2.0
+ - plotly=5.13.1
+ - pluggy=1.0.0
+ - ply=3.11
+ - pooch=1.7.0
+ - prompt-toolkit=3.0.38
+ - psutil=5.9.4
+ - ptyprocess=0.7.0
+ - pulp=2.7.0
+ - pure_eval=0.2.2
+ - py2bit=0.3.0
+ - pybedtools=0.9.0
+ - pybigwig=0.3.18
+ - pycparser=2.21
+ - pyfaidx=0.7.2.1
+ - pygments=2.14.0
+ - pyopenssl=23.1.1
+ - pyparsing=3.0.9
+ - pyqt=5.15.7
+ - pyqt5-sip=12.11.0
+ - pyrsistent=0.19.3
+ - pysam=0.20.0
+ - pysocks=1.7.1
+ - pytest=7.2.2
+ - pytest-xdist=3.2.1
+ - python-dateutil=2.8.2
+ - python-lzo=1.14
+ - pytz=2023.3
+ - pyvcf3=1.0.3
+ - pyyaml=6.0
+ - requests=2.28.2
+ - reretry=0.11.8
+ - rich=13.3.3
+ - rich-click=1.6.1
+ - rseqc=5.0.1
+ - scipy=1.10.1
+ - seaborn=0.12.2
+ - setuptools=67.6.1
+ - simplejson=3.18.4
+ - sip=6.7.7
+ - six=1.16.0
+ - smart-open=6.3.0
+ - smmap=3.0.5
+ - snakemake=7.25.0
+ - spectra=0.0.11
+ - stack_data=0.6.2
+ - statsmodels=0.13.5
+ - stopit=1.1.2
+ - tabulate=0.9.0
+ - tenacity=8.2.2
+ - throttler=1.2.1
+ - toml=0.10.2
+ - tomli=2.0.1
+ - toposort=1.10
+ - tornado=6.2
+ - trackhub=0.2.4
+ - traitlets=5.9.0
+ - typing-extensions=4.5.0
+ - unicodedata2=15.0.0
+ - urllib3=1.26.15
+ - wcwidth=0.2.6
+ - wheel=0.40.0
+ - wrapt=1.15.0
+ - xopen=1.7.0
+ - yte=1.5.1
+ - zipp=3.15.0
+ - zstandard=0.19.0
From f48e7a7fbd90a5936b44b081a9b572caa2575e1a Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Thu, 30 Mar 2023 08:46:54 -0400
Subject: [PATCH 66/91] update broken ERCC link
---
include/reference_configs/ERCC.yaml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/include/reference_configs/ERCC.yaml b/include/reference_configs/ERCC.yaml
index cea79ccc..22aa25af 100644
--- a/include/reference_configs/ERCC.yaml
+++ b/include/reference_configs/ERCC.yaml
@@ -2,14 +2,14 @@ references:
ercc:
srm2374:
genome:
- url: 'https://www-s.nist.gov/srmors/certificates/documents/SRM2374_Sequence_v1.FASTA'
+ url: 'https://tsapps.nist.gov/srmext/certificates/documents/SRM2374_Sequence_v1.FASTA'
postprocess: "lib.postprocess.ercc.fasta_postprocess"
indexes:
- 'bowtie2'
- 'hisat2'
- 'star'
annotation:
- url: 'https://www-s.nist.gov/srmors/certificates/documents/SRM2374_Sequence_v1.FASTA'
+ url: 'https://tsapps.nist.gov/srmext/certificates/documents/SRM2374_Sequence_v1.FASTA'
postprocess: "lib.postprocess.ercc.gtf_postprocess"
fisher92:
From 682cf2a7ae971675c2b6e3bcf7b61b1bad536feb Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Thu, 30 Mar 2023 10:47:41 -0400
Subject: [PATCH 67/91] fix salmon version requirements
---
env.yml | 386 +++++++++++++++++++++++++++++---------------------------
1 file changed, 197 insertions(+), 189 deletions(-)
diff --git a/env.yml b/env.yml
index a47dcab5..e7d7a61f 100644
--- a/env.yml
+++ b/env.yml
@@ -5,120 +5,168 @@ dependencies:
- _libgcc_mutex=0.1
- _openmp_mutex=4.5
- _r-mutex=1.0.1
- - alsa-lib=1.2.8
+ - alsa-lib=1.2.3.2
+ - amply=0.1.5
+ - appdirs=1.4.4
+ - argcomplete=3.0.5
+ - argh=0.27.2
+ - asttokens=2.2.1
- attr=2.5.1
+ - attrs=22.2.0
+ - backcall=0.2.0
- backports=1.0
- backports.functools_lru_cache=1.6.4
- bedtools=2.30.0
- - binutils_impl_linux-64=2.40
+ - binutils_impl_linux-64=2.39
+ - binutils_linux-64=2.39
+ - biopython=1.81
+ - boost-cpp=1.74.0
- bowtie=1.3.1
- bowtie2=2.5.1
- brotli=1.0.9
- brotli-bin=1.0.9
+ - brotlipy=0.7.0
- bwidget=1.9.14
+ - bx-python=0.9.0
- bzip2=1.0.8
- c-ares=1.18.1
- ca-certificates=2022.12.7
- cairo=1.16.0
+ - certifi=2022.12.7
+ - cffi=1.15.1
+ - charset-normalizer=2.1.1
+ - click=8.1.3
- coin-or-cbc=2.10.8
- coin-or-cgl=0.60.6
- coin-or-clp=1.17.7
- coin-or-osi=0.108.7
- coin-or-utils=2.11.6
- coincbc=2.10.8
+ - colorama=0.4.6
+ - coloredlogs=15.0.1
+ - colormath=3.0.0
+ - configargparse=1.5.3
- connection_pool=0.0.3
- - curl=7.87.0
+ - contourpy=1.0.7
+ - cryptography=39.0.0
+ - curl=7.86.0
+ - cutadapt=4.3
+ - cycler=0.11.0
+ - datrie=0.8.2
- dbus=1.13.6
+ - decorator=5.1.1
+ - deeptools=3.5.1
+ - deeptoolsintervals=0.1.9
+ - dnaio=0.10.0
+ - docutils=0.19
+ - dpath=2.1.5
+ - exceptiongroup=1.1.1
+ - execnet=1.9.0
+ - executing=1.2.0
- expat=2.5.0
- fastq-screen=0.15.2
- fastqc=0.12.1
- fftw=3.3.10
+ - filelock=3.10.7
- font-ttf-dejavu-sans-mono=2.37
- font-ttf-inconsolata=3.000
- font-ttf-source-code-pro=2.038
- font-ttf-ubuntu=0.83
- fontconfig=2.14.2
- - fonts-conda-ecosystem=1=0
- - fonts-conda-forge=1=0
+ - fonts-conda-ecosystem=1
+ - fonts-conda-forge=1
+ - fonttools=4.39.3
- freetype=2.12.1
- fribidi=1.0.10
- - gcc_impl_linux-64=12.2.0
+ - future=0.18.3
+ - gat=1.3.6
+ - gcc_impl_linux-64=10.4.0
+ - gcc_linux-64=10.4.0
- gettext=0.21.1
- gffread=0.12.7
- - gfortran_impl_linux-64=12.2.0
+ - gffutils=0.11.1
+ - gfortran_impl_linux-64=10.4.0
+ - gfortran_linux-64=10.4.0
- giflib=5.2.1
+ - gitdb=4.0.10
+ - gitpython=3.1.31
- glib=2.74.1
- glib-tools=2.74.1
- graphite2=1.3.13
- gsl=2.7
- - gst-plugins-base=1.21.3
- - gstreamer=1.21.3
- - gstreamer-orc=0.4.33
- - gxx_impl_linux-64=12.2.0
- - harfbuzz=6.0.0
+ - gst-plugins-base=1.18.5
+ - gstreamer=1.20.3
+ - gxx_impl_linux-64=10.4.0
+ - gxx_linux-64=10.4.0
+ - harfbuzz=4.2.0
- hdf5=1.12.1
- hisat2=2.2.1
- - htslib=1.17
- - icu=70.1
+ - htslib=1.16
+ - humanfriendly=10.0
+ - icu=69.1
+ - idna=3.4
+ - importlib-metadata=6.1.0
- importlib_resources=5.12.0
- - intervalstats=1.01=0
+ - iniconfig=2.0.0
+ - intervalstats=1.01
+ - ipython=8.11.0
- isa-l=2.30.0
- - jack=1.9.22
+ - jack=1.9.18
+ - jedi=0.18.2
+ - jinja2=3.1.2
- jpeg=9e
+ - jsonschema=4.17.3
- jupyter_core=5.3.0
- kallisto=0.48.0
- kernel-headers_linux-64=2.6.32
- keyutils=1.6.1
- - krb5=1.20.1
- - lame=3.100
+ - kiwisolver=1.4.4
+ - krb5=1.19.3
- lcms2=2.14
- - ld_impl_linux-64=2.40
+ - ld_impl_linux-64=2.39
- lerc=4.0.0
- libblas=3.9.0
- libbrotlicommon=1.0.9
- libbrotlidec=1.0.9
- libbrotlienc=1.0.9
- - libcap=2.66
+ - libcap=2.64
- libcblas=3.9.0
- - libclang=15.0.7
- - libclang13=15.0.7
+ - libclang=13.0.1
- libcups=2.3.3
- - libcurl=7.87.0
+ - libcurl=7.86.0
- libdb=6.2.32
- libdeflate=1.13
- libedit=3.1.20191231
- libev=4.33
- libevent=2.1.10
- libffi=3.4.2
- - libflac=1.4.2
- - libgcc-devel_linux-64=12.2.0
+ - libflac=1.3.4
+ - libgcc-devel_linux-64=10.4.0
- libgcc-ng=12.2.0
- - libgcrypt=1.10.1
- libgd=2.3.3
- libgfortran-ng=12.2.0
- libgfortran5=12.2.0
- libglib=2.74.1
- libgomp=12.2.0
- - libgpg-error=1.46
- - libhwloc=2.9.0
+ - libhwloc=2.8.0
- libiconv=1.17
+ - libjemalloc=5.3.0
- liblapack=3.9.0
- liblapacke=3.9.0
- - libllvm15=15.0.7
+ - libllvm13=13.0.1
- libnghttp2=1.51.0
- libnsl=2.0.0
- libogg=1.3.4
- libopenblas=0.3.21
- libopus=1.3.1
- libpng=1.6.39
- - libpq=15.1
- - libsanitizer=12.2.0
- - libsndfile=1.2.0
+ - libpq=14.5
+ - libsanitizer=10.4.0
+ - libsndfile=1.0.31
- libsqlite=3.40.0
- libssh2=1.10.0
- - libstdcxx-devel_linux-64=12.2.0
+ - libstdcxx-devel_linux-64=10.4.0
- libstdcxx-ng=12.2.0
- - libsystemd0=252
- libtiff=4.4.0
- libtool=2.4.7
- libudev1=253
@@ -127,187 +175,99 @@ dependencies:
- libwebp=1.2.4
- libwebp-base=1.2.4
- libxcb=1.13
- - libxkbcommon=1.5.0
- - libxml2=2.10.3
+ - libxkbcommon=1.0.3
+ - libxml2=2.9.14
- libzlib=1.2.13
- - lz4-c=1.9.4
- lzo=2.10
- - make=4.3
- - matplotlib-base=3.7.1
- - mpg123=1.31.3
- - mysql-common=8.0.32
- - mysql-connector-c=6.1.11
- - mysql-libs=8.0.32
- - ncurses=6.3
- - nspr=4.35
- - nss=3.89
- - openjdk=17.0.3
- - openjpeg=2.5.0
- - openssl=1.1.1t
- - pandoc=3.1.1
- - pango=1.50.14
- - pbzip2=1.1.13=0
- - pcre2=10.40
- - perl=5.32.1
- - perl-gd=2.76
- - perl-gdgraph=1.54
- - perl-gdtextutil=0.86
- - picard=3.0.0
- - pigz=2.6
- - pixman=0.40.0
- - preseq=3.2.0
- - prompt_toolkit=3.0.38
- - pthread-stubs=0.4
- - pulseaudio=16.1
- - pure_eval=0.2.2
- - pyqt=5.15.7
- - python=3.10.8
- - python-fastjsonschema=2.16.3
- - python-isal=1.1.0
- - python_abi=3.10=3_cp310
- - qt-main=5.15.6
- - r-base=4.2.2
- - readline=8.2
- - salmon=0.8.1=0
- - samtools=1.16.1
- - seaborn-base=0.12.2
- - sed=4.8
- - smart_open=6.3.0
- - snakemake-minimal=7.25.0
- - sra-tools=2.9.6
- - stack_data=0.6.2
- - star=2.7.10b
- - subread=2.0.3
- - sysroot_linux-64=2.12
- - tbb=2021.8.0
- - tk=8.6.12
- - tktable=2.10
- - typing_extensions=4.5.0
- - tzdata=2023c
- - ucsc-bedgraphtobigwig=377
- - ucsc-bedsort=377
- - ucsc-bedtobigbed=377
- - ucsc-bigwigmerge=377
- - ucsc-fetchchromsizes=377
- - ucsc-genepredtobed=377
- - ucsc-gtftogenepred=377
- - ucsc-liftover=377
- - ucsc-oligomatch=377
- - ucsc-twobittofa=377
- - ucsc-wigtobigwig=377
- - xcb-util=0.4.0
- - xcb-util-image=0.4.0
- - xcb-util-keysyms=0.4.0
- - xcb-util-renderutil=0.3.9
- - xcb-util-wm=0.4.1
- - xkeyboard-config=2.38
- - xorg-fixesproto=5.0
- - xorg-inputproto=2.3.2
- - xorg-kbproto=1.0.7
- - xorg-libice=1.0.10
- - xorg-libsm=1.2.3
- - xorg-libx11=1.8.4
- - xorg-libxau=1.0.9
- - xorg-libxdmcp=1.1.3
- - xorg-libxext=1.3.4
- - xorg-libxfixes=5.0.3
- - xorg-libxi=1.7.10
- - xorg-libxrender=0.9.10
- - xorg-libxt=1.2.1
- - xorg-libxtst=1.2.3
- - xorg-recordproto=1.14.2
- - xorg-renderproto=0.11.1
- - xorg-xextproto=7.3.0
- - xorg-xproto=7.0.31
- - xz=5.2.6
- - yaml=0.2.5
- - zlib=1.2.13
- - zstd=1.5.2
- - amply=0.1.5
- - appdirs=1.4.4
- - argcomplete=3.0.5
- - argh=0.27.2
- - asttokens=2.2.1
- - attrs=22.2.0
- - backcall=0.2.0
- - backports.functools_lru_cache=1.6.4
- - biopython=1.81
- - brotlipy=0.7.0
- - bx-python=0.9.0
- - certifi=2022.12.7
- - cffi=1.15.1
- - charset-normalizer=2.1.1
- - click=8.1.3
- - colorama=0.4.6
- - coloredlogs=15.0.1
- - colormath=3.0.0
- - configargparse=1.5.3
- - connection_pool=0.0.3
- - contourpy=1.0.7
- - cryptography=39.0.0
- - cutadapt=4.3
- - cycler=0.11.0
- - datrie=0.8.2
- - decorator=5.1.1
- - deeptools=3.5.1
- - deeptoolsintervals=0.1.9
- - dnaio=0.10.0
- - docutils=0.19
- - dpath=2.1.5
- - exceptiongroup=1.1.1
- - execnet=1.9.0
- - executing=1.2.0
- - python-fastjsonschema=2.16.3
- - filelock=3.10.7
- - fonttools=4.39.3
- - future=0.18.3
- - gat=1.3.6
- - gffutils=0.11.1
- - gitdb=4.0.10
- - gitpython=3.1.31
- - humanfriendly=10.0
- - idna=3.4
- - importlib-metadata=6.1.0
- - importlib-resources=5.12.0
- - iniconfig=2.0.0
- - ipython=8.11.0
- - python-isal=1.1.0
- - jedi=0.18.2
- - jinja2=3.1.2
- - jsonschema=4.17.3
- - jupyter_core=5.3.0
- - kiwisolver=1.4.4
- lzstring=1.0.4
+ - make=4.3
- markdown=3.4.3
- markdown-it-py=2.2.0
- markupsafe=2.1.2
- matplotlib=3.7.1
+ - matplotlib-base=3.7.1
- matplotlib-inline=0.1.6
- mdurl=0.1.0
- multiqc=1.14
- munkres=1.1.4
+ - mysql-common=8.0.32
+ - mysql-connector-c=6.1.11
+ - mysql-libs=8.0.32
- nbformat=5.8.0
+ - ncbi-vdb=3.0.2
+ - ncurses=6.3
- networkx=3.0
+ - nspr=4.35
+ - nss=3.89
- numpy=1.23.5
+ - openjdk=11.0.1
+ - openjpeg=2.5.0
+ - openssl=1.1.1t
+ - ossuuid=1.6.2
- packaging=23.0
- pandas=1.5.3
+ - pandoc=3.1.1
+ - pango=1.50.7
- parso=0.8.3
- patsy=0.5.3
+ - pbzip2=1.1.13
+ - pcre2=10.37
+ - perl=5.32.1
+ - perl-alien-build=2.48
+ - perl-alien-libxml2=0.17
+ - perl-business-isbn=3.007
+ - perl-business-isbn-data=20210112.006
+ - perl-capture-tiny=0.48
+ - perl-carp=1.50
+ - perl-constant=1.33
+ - perl-data-dumper=2.183
+ - perl-encode=3.19
+ - perl-exporter=5.74
+ - perl-extutils-makemaker=7.70
+ - perl-ffi-checklib=0.28
+ - perl-file-chdir=0.1011
+ - perl-file-path=2.18
+ - perl-file-temp=0.2304
+ - perl-file-which=1.24
+ - perl-gd=2.76
+ - perl-gdgraph=1.54
+ - perl-gdtextutil=0.86
+ - perl-importer=0.026
+ - perl-mime-base64=3.16
+ - perl-parent=0.241
+ - perl-path-tiny=0.124
+ - perl-pathtools=3.75
+ - perl-scope-guard=0.21
+ - perl-storable=3.15
+ - perl-sub-info=0.002
+ - perl-term-table=0.016
+ - perl-test2-suite=0.000145
+ - perl-uri=5.12
+ - perl-xml-libxml=2.0207
+ - perl-xml-namespacesupport=1.12
+ - perl-xml-sax=1.02
+ - perl-xml-sax-base=1.09
- pexpect=4.8.0
+ - picard=3.0.0
- pickleshare=0.7.5
+ - pigz=2.6
- pillow=9.2.0
- pip=23.0.1
+ - pixman=0.40.0
- pkgutil-resolve-name=1.3.10
- plac=1.3.5
- platformdirs=3.2.0
- - plotly=5.13.1
+ - plotly=5.14.0
- pluggy=1.0.0
- - ply=3.11
- pooch=1.7.0
+ - preseq=3.2.0
- prompt-toolkit=3.0.38
+ - prompt_toolkit=3.0.38
- psutil=5.9.4
+ - pthread-stubs=0.4
- ptyprocess=0.7.0
- pulp=2.7.0
+ - pulseaudio=14.0
- pure_eval=0.2.2
- py2bit=0.3.0
- pybedtools=0.9.0
@@ -317,39 +277,58 @@ dependencies:
- pygments=2.14.0
- pyopenssl=23.1.1
- pyparsing=3.0.9
- - pyqt=5.15.7
- - pyqt5-sip=12.11.0
+ - pyqt=5.15.4
+ - pyqt5-sip=12.9.0
- pyrsistent=0.19.3
- pysam=0.20.0
- pysocks=1.7.1
- pytest=7.2.2
- pytest-xdist=3.2.1
+ - python=3.10.8
- python-dateutil=2.8.2
+ - python-fastjsonschema=2.16.3
+ - python-isal=1.1.0
- python-lzo=1.14
+ - python_abi=3.10
- pytz=2023.3
- pyvcf3=1.0.3
- pyyaml=6.0
+ - qt-main=5.15.2
+ - r-base=4.1.3
+ - readline=8.2
- requests=2.28.2
- reretry=0.11.8
- rich=13.3.3
- rich-click=1.6.1
- rseqc=5.0.1
+ - salmon=1.10.1
+ - samtools=1.16.1
- scipy=1.10.1
- seaborn=0.12.2
+ - seaborn-base=0.12.2
+ - sed=4.8
- setuptools=67.6.1
- simplejson=3.18.4
- - sip=6.7.7
+ - sip=6.5.1
- six=1.16.0
- - smart-open=6.3.0
+ - smart_open=6.3.0
- smmap=3.0.5
- - snakemake=7.25.0
+ - snakemake-minimal=7.25.0
- spectra=0.0.11
+ - sqlite=3.40.0
+ - sra-tools=3.0.3
- stack_data=0.6.2
+ - star=2.7.10b
- statsmodels=0.13.5
- stopit=1.1.2
+ - subread=2.0.3
+ - sysroot_linux-64=2.12
- tabulate=0.9.0
+ - tbb=2021.7.0
- tenacity=8.2.2
- throttler=1.2.1
+ - tk=8.6.12
+ - tktable=2.10
- toml=0.10.2
- tomli=2.0.1
- toposort=1.10
@@ -357,12 +336,41 @@ dependencies:
- trackhub=0.2.4
- traitlets=5.9.0
- typing-extensions=4.5.0
+ - typing_extensions=4.5.0
+ - tzdata=2023c
+ - ucsc-bedgraphtobigwig=377
+ - ucsc-bedsort=377
+ - ucsc-bedtobigbed=377
+ - ucsc-bigwigmerge=377
+ - ucsc-fetchchromsizes=377
+ - ucsc-genepredtobed=377
+ - ucsc-gtftogenepred=377
+ - ucsc-liftover=377
+ - ucsc-oligomatch=377
+ - ucsc-twobittofa=377
+ - ucsc-wigtobigwig=377
- unicodedata2=15.0.0
- urllib3=1.26.15
- wcwidth=0.2.6
- wheel=0.40.0
- wrapt=1.15.0
- xopen=1.7.0
+ - xorg-kbproto=1.0.7
+ - xorg-libice=1.0.10
+ - xorg-libsm=1.2.3
+ - xorg-libx11=1.8.4
+ - xorg-libxau=1.0.9
+ - xorg-libxdmcp=1.1.3
+ - xorg-libxext=1.3.4
+ - xorg-libxrender=0.9.10
+ - xorg-libxt=1.2.1
+ - xorg-renderproto=0.11.1
+ - xorg-xextproto=7.3.0
+ - xorg-xproto=7.0.31
+ - xz=5.2.6
+ - yaml=0.2.5
- yte=1.5.1
- zipp=3.15.0
+ - zlib=1.2.13
- zstandard=0.19.0
+ - zstd=1.5.2
From 1c15b7e3f042ae0e3bbe12c211418f2bfabe716f Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Thu, 30 Mar 2023 10:48:22 -0400
Subject: [PATCH 68/91] update conda upon requirements updates
---
.circleci/config.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index d5d62086..43c35896 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -69,6 +69,7 @@ variables:
# exist.
if ! conda env list | grep -q "lcdb-wf-test"; then
echo "Setting up conda..."
+ conda update conda
conda config --system --add channels defaults
conda config --system --add channels bioconda
conda config --system --add channels conda-forge
From 7071724324bbf7004168f9a8f7e2fa2c315f464f Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Thu, 30 Mar 2023 15:38:10 -0400
Subject: [PATCH 69/91] fix picard version
---
env.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/env.yml b/env.yml
index e7d7a61f..211aed41 100644
--- a/env.yml
+++ b/env.yml
@@ -248,7 +248,7 @@ dependencies:
- perl-xml-sax=1.02
- perl-xml-sax-base=1.09
- pexpect=4.8.0
- - picard=3.0.0
+ - picard=2.27.4
- pickleshare=0.7.5
- pigz=2.6
- pillow=9.2.0
From d11e54dc13bb4c9fe7a69bb711692a0a8068a00c Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Thu, 30 Mar 2023 16:35:33 -0400
Subject: [PATCH 70/91] debug tests
---
.circleci/config.yml | 69 ++++++++++++++++++++++----------------------
1 file changed, 35 insertions(+), 34 deletions(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 43c35896..fb16899e 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -67,6 +67,7 @@ variables:
source $BASH_ENV
# We only do the installation if the conda environment does not already
# exist.
+ mamba --version
if ! conda env list | grep -q "lcdb-wf-test"; then
echo "Setting up conda..."
conda update conda
@@ -403,41 +404,41 @@ workflows:
test-suite:
jobs:
- initial-setup
- - pytest:
- requires:
- - initial-setup
- - chipseq:
- requires:
- - initial-setup
- - pytest
+# - pytest:
+# requires:
+# - initial-setup
+# - chipseq:
+# requires:
+# - initial-setup
+# - pytest
- chipseq-misc:
requires:
- initial-setup
- pytest
- - rnaseq:
- requires:
- - initial-setup
- - pytest
- - rnaseq-misc:
- requires:
- - initial-setup
- - pytest
- - references:
- requires:
- - initial-setup
- - pytest
- - colocalization:
- requires:
- - initial-setup
- - pytest
- - build-docs:
- requires:
- - initial-setup
- - report-env:
- requires:
- - rnaseq
- - rnaseq-misc
- - chipseq
- - chipseq-misc
- - references
- - colocalization
+# - rnaseq:
+# requires:
+# - initial-setup
+# - pytest
+# - rnaseq-misc:
+# requires:
+# - initial-setup
+# - pytest
+# - references:
+# requires:
+# - initial-setup
+# - pytest
+# - colocalization:
+# requires:
+# - initial-setup
+# - pytest
+# - build-docs:
+# requires:
+# - initial-setup
+# - report-env:
+# requires:
+# - rnaseq
+# - rnaseq-misc
+# - chipseq
+# - chipseq-misc
+# - references
+# - colocalization
From a13c805997a8cdbb4e58191b7eabae4bb7b5f945 Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Thu, 30 Mar 2023 16:38:26 -0400
Subject: [PATCH 71/91] debug tests
---
.circleci/config.yml | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index fb16899e..63ecebe9 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -404,9 +404,9 @@ workflows:
test-suite:
jobs:
- initial-setup
-# - pytest:
-# requires:
-# - initial-setup
+ - pytest:
+ requires:
+ - initial-setup
# - chipseq:
# requires:
# - initial-setup
From 9a3d6296efc7a8a7ba24cdb880a8b905c1e970d9 Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Fri, 31 Mar 2023 06:03:49 -0400
Subject: [PATCH 72/91] debug tests
---
.circleci/config.yml | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 63ecebe9..b15f7be7 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -67,7 +67,8 @@ variables:
source $BASH_ENV
# We only do the installation if the conda environment does not already
# exist.
- mamba --version
+ conda env export | grep mamba
+ exit 1
if ! conda env list | grep -q "lcdb-wf-test"; then
echo "Setting up conda..."
conda update conda
From 154904aed123af944486b289ddc34df61d6f8145 Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Fri, 31 Mar 2023 06:11:09 -0400
Subject: [PATCH 73/91] debug tests
---
.circleci/config.yml | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index b15f7be7..dc3bc117 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -67,7 +67,8 @@ variables:
source $BASH_ENV
# We only do the installation if the conda environment does not already
# exist.
- conda env export | grep mamba
+ conda env export | grep glib
+ which mamba
exit 1
if ! conda env list | grep -q "lcdb-wf-test"; then
echo "Setting up conda..."
From 5069a7d748cd6f37ab99f00ab5cf5f229d6e4e37 Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Fri, 31 Mar 2023 06:18:56 -0400
Subject: [PATCH 74/91] debug tests
---
.circleci/config.yml | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index dc3bc117..eb6ddd9a 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -67,7 +67,9 @@ variables:
source $BASH_ENV
# We only do the installation if the conda environment does not already
# exist.
- conda env export | grep glib
+ conda env export | grep libc
+ conda env export | grep mamba
+ conda env list
which mamba
exit 1
if ! conda env list | grep -q "lcdb-wf-test"; then
From b5e5fb757948fe996e6b03ca0a5ce77fc47be54f Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Fri, 31 Mar 2023 06:25:50 -0400
Subject: [PATCH 75/91] debug tests
---
.circleci/config.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index eb6ddd9a..5dd6c03b 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -71,6 +71,7 @@ variables:
conda env export | grep mamba
conda env list
which mamba
+ mamba --version
exit 1
if ! conda env list | grep -q "lcdb-wf-test"; then
echo "Setting up conda..."
From 06c5d9a7abd4de657b85fe3d02baf3e3dfdf23af Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Fri, 31 Mar 2023 10:10:14 -0400
Subject: [PATCH 76/91] debug tests
---
.circleci/config.yml | 12 +++++-------
1 file changed, 5 insertions(+), 7 deletions(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 5dd6c03b..e01a72f7 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -26,7 +26,7 @@ variables:
save_cache: &save_cache
save_cache:
- key: v0-{{ checksum "env.yml" }}-{{ checksum "env-r.yml" }}
+ key: v1-{{ checksum "env.yml" }}-{{ checksum "env-r.yml" }}
paths:
- /opt/conda
@@ -49,7 +49,7 @@ variables:
command: |
# x11-utils required to avoid R::png() segfaulting
apt update && apt install -y locales-all locales rsync x11-utils
- conda install -y yaml
+ conda install -y yaml gcc
echo 'export DEPLOY=/tmp/lcdb-wf-test' >> $BASH_ENV
echo 'export LCDBWF_ENV=lcdb-wf-test' >> $BASH_ENV
echo 'export LCDBWF_ENV_R=lcdb-wf-test-r' >> $BASH_ENV
@@ -67,19 +67,17 @@ variables:
source $BASH_ENV
# We only do the installation if the conda environment does not already
# exist.
- conda env export | grep libc
conda env export | grep mamba
conda env list
- which mamba
- mamba --version
- exit 1
if ! conda env list | grep -q "lcdb-wf-test"; then
echo "Setting up conda..."
conda update conda
conda config --system --add channels defaults
conda config --system --add channels bioconda
conda config --system --add channels conda-forge
- conda install mamba yaml -y
+ conda install gcc mamba yaml -y
+ which mamba
+ mamba --version
mamba env create -n $LCDBWF_ENV --file env.yml
mamba env create -n $LCDBWF_ENV_R --file env-r.yml
fi
From cd6caf40647f83a84f07977a311bc3502d97632b Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Fri, 31 Mar 2023 10:21:39 -0400
Subject: [PATCH 77/91] debug tests
---
.circleci/config.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index e01a72f7..3ff2d04c 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -49,7 +49,7 @@ variables:
command: |
# x11-utils required to avoid R::png() segfaulting
apt update && apt install -y locales-all locales rsync x11-utils
- conda install -y yaml gcc
+ conda install -y yaml
echo 'export DEPLOY=/tmp/lcdb-wf-test' >> $BASH_ENV
echo 'export LCDBWF_ENV=lcdb-wf-test' >> $BASH_ENV
echo 'export LCDBWF_ENV_R=lcdb-wf-test-r' >> $BASH_ENV
From bc2aacaf1be830867405fa1ea311b433f1455acb Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Fri, 31 Mar 2023 10:30:16 -0400
Subject: [PATCH 78/91] debug tests
---
.circleci/config.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 3ff2d04c..97b222fc 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -38,7 +38,7 @@ variables:
restore_cache: &restore_cache
restore_cache:
keys:
- - v0-{{ checksum "env.yml" }}-{{ checksum "env-r.yml" }}
+ - v1-{{ checksum "env.yml" }}-{{ checksum "env-r.yml" }}
# --------------------------------------------------------------------------
# The path needs to be set each time; in jobs below this will be called as
From a93b30add9634d027136cb47ee0d0f624102c119 Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Fri, 31 Mar 2023 10:39:02 -0400
Subject: [PATCH 79/91] debug tests
---
.circleci/config.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 97b222fc..c18413a3 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -26,7 +26,7 @@ variables:
save_cache: &save_cache
save_cache:
- key: v1-{{ checksum "env.yml" }}-{{ checksum "env-r.yml" }}
+ key: v2-{{ checksum "env.yml" }}-{{ checksum "env-r.yml" }}
paths:
- /opt/conda
From 53bb131669d4fdfc829825645877d95c57eebc17 Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Fri, 31 Mar 2023 10:53:08 -0400
Subject: [PATCH 80/91] trigger rebuilding envs
---
env.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/env.yml b/env.yml
index 211aed41..4594f5ea 100644
--- a/env.yml
+++ b/env.yml
@@ -374,3 +374,4 @@ dependencies:
- zlib=1.2.13
- zstandard=0.19.0
- zstd=1.5.2
+#
From 13d9c2c4376a3b8739707bcedd6211683a3dc2e0 Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Fri, 31 Mar 2023 11:52:35 -0400
Subject: [PATCH 81/91] debug tests
---
.circleci/config.yml | 4 +---
1 file changed, 1 insertion(+), 3 deletions(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index c18413a3..b7285000 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -26,7 +26,7 @@ variables:
save_cache: &save_cache
save_cache:
- key: v2-{{ checksum "env.yml" }}-{{ checksum "env-r.yml" }}
+ key: v0-{{ checksum "env.yml" }}-{{ checksum "env-r.yml" }}
paths:
- /opt/conda
@@ -67,8 +67,6 @@ variables:
source $BASH_ENV
# We only do the installation if the conda environment does not already
# exist.
- conda env export | grep mamba
- conda env list
if ! conda env list | grep -q "lcdb-wf-test"; then
echo "Setting up conda..."
conda update conda
From 99663a6a115f5645f843b88c8c311a982c22518d Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Fri, 31 Mar 2023 12:26:26 -0400
Subject: [PATCH 82/91] debug tests
---
.circleci/config.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index b7285000..083d65ab 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -86,6 +86,7 @@ variables:
run:
name: Download example data
command: |
+ conda info --envs
source activate lcdb-wf-test
# rsync is required for the deployment process
From 9811f88b89631416f69e130e542cec3016188738 Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Fri, 31 Mar 2023 12:56:35 -0400
Subject: [PATCH 83/91] debug tests
---
.circleci/config.yml | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 083d65ab..98a56985 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -433,9 +433,9 @@ workflows:
# requires:
# - initial-setup
# - pytest
-# - build-docs:
-# requires:
-# - initial-setup
+ - build-docs:
+ requires:
+ - initial-setup
# - report-env:
# requires:
# - rnaseq
From 44512091e0e4fd688694eeaff152aca65c72fd51 Mon Sep 17 00:00:00 2001
From: Caroline Esnault <caroline.esnault@nih.gov>
Date: Fri, 31 Mar 2023 13:15:38 -0400
Subject: [PATCH 84/91] trigger new cache
---
.circleci/config.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 98a56985..3d3e72b9 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -26,7 +26,7 @@ variables:
save_cache: &save_cache
save_cache:
- key: v0-{{ checksum "env.yml" }}-{{ checksum "env-r.yml" }}
+ key: v3-{{ checksum "env.yml" }}-{{ checksum "env-r.yml" }}
paths:
- /opt/conda
From 34408bbc599722a7522f26e3655411cc8e750449 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Sun, 2 Apr 2023 10:18:07 -0400
Subject: [PATCH 85/91] align save/restore caches
---
.circleci/config.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 3d3e72b9..4595e48b 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -38,7 +38,7 @@ variables:
restore_cache: &restore_cache
restore_cache:
keys:
- - v1-{{ checksum "env.yml" }}-{{ checksum "env-r.yml" }}
+ - v3-{{ checksum "env.yml" }}-{{ checksum "env-r.yml" }}
# --------------------------------------------------------------------------
# The path needs to be set each time; in jobs below this will be called as
From 5e483a993a185a05cd71c51c236cf6286c0df666 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Sun, 2 Apr 2023 10:23:06 -0400
Subject: [PATCH 86/91] invalidate cache
---
.circleci/config.yml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 4595e48b..71f7a0a5 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -26,7 +26,7 @@ variables:
save_cache: &save_cache
save_cache:
- key: v3-{{ checksum "env.yml" }}-{{ checksum "env-r.yml" }}
+ key: v4-{{ checksum "env.yml" }}-{{ checksum "env-r.yml" }}
paths:
- /opt/conda
@@ -38,7 +38,7 @@ variables:
restore_cache: &restore_cache
restore_cache:
keys:
- - v3-{{ checksum "env.yml" }}-{{ checksum "env-r.yml" }}
+ - v4-{{ checksum "env.yml" }}-{{ checksum "env-r.yml" }}
# --------------------------------------------------------------------------
# The path needs to be set each time; in jobs below this will be called as
From 0e375d466cfb0b647f04596d42080207e91f35a9 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Sun, 2 Apr 2023 10:23:17 -0400
Subject: [PATCH 87/91] don't need to install yaml so early
---
.circleci/config.yml | 1 -
1 file changed, 1 deletion(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 71f7a0a5..d36b5f71 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -49,7 +49,6 @@ variables:
command: |
# x11-utils required to avoid R::png() segfaulting
apt update && apt install -y locales-all locales rsync x11-utils
- conda install -y yaml
echo 'export DEPLOY=/tmp/lcdb-wf-test' >> $BASH_ENV
echo 'export LCDBWF_ENV=lcdb-wf-test' >> $BASH_ENV
echo 'export LCDBWF_ENV_R=lcdb-wf-test-r' >> $BASH_ENV
From de03bffca9daea09e12d023c557b875d6c7606c5 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Sun, 2 Apr 2023 10:23:28 -0400
Subject: [PATCH 88/91] set strict channel priority
---
.circleci/config.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index d36b5f71..67bcb040 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -72,6 +72,7 @@ variables:
conda config --system --add channels defaults
conda config --system --add channels bioconda
conda config --system --add channels conda-forge
+ conda config --system --set channel_priority strict
conda install gcc mamba yaml -y
which mamba
mamba --version
From 6452bcc9aff8b6993c386bf38ed161323fa5bffd Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Sun, 2 Apr 2023 10:23:44 -0400
Subject: [PATCH 89/91] streamline jobs for tighter feedback loop when
troubleshooting
---
.circleci/config.yml | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 67bcb040..f28289a4 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -406,9 +406,9 @@ workflows:
test-suite:
jobs:
- initial-setup
- - pytest:
- requires:
- - initial-setup
+# - pytest:
+# requires:
+# - initial-setup
# - chipseq:
# requires:
# - initial-setup
@@ -416,7 +416,7 @@ workflows:
- chipseq-misc:
requires:
- initial-setup
- - pytest
+# - pytest
# - rnaseq:
# requires:
# - initial-setup
@@ -433,9 +433,9 @@ workflows:
# requires:
# - initial-setup
# - pytest
- - build-docs:
- requires:
- - initial-setup
+# - build-docs:
+# requires:
+# - initial-setup
# - report-env:
# requires:
# - rnaseq
From 5f7dfffc1dd13ce65c650777cb61086fd3d1970e Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Sun, 2 Apr 2023 10:46:08 -0400
Subject: [PATCH 90/91] try an actual test with gh actions
---
.github/workflows/main.yaml | 48 ++++++++++++++++++++++++++++++++++---
1 file changed, 45 insertions(+), 3 deletions(-)
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
index 9d4581eb..058e9590 100644
--- a/.github/workflows/main.yaml
+++ b/.github/workflows/main.yaml
@@ -1,4 +1,11 @@
on: [push]
+env:
+ DEPLOY: /tmp/lcdb-wf-test
+ LCDBWF_ENV: lcdb-wf-test
+ LCDBWF_ENV_R: lcdb-wf-test-r
+ LC_ALL: en_US.utf8
+ LANG: en_US.utf8
+
jobs:
build:
@@ -29,8 +36,43 @@ jobs:
mamba env create -n lcdb-wf-test --file env.yml
mamba env create -n lcdb-wf-test-r --file env-r.yml
- - name: STAR available?
- shell: bash
+ - name: Download example data
+ run: |
+ conda info --envs
+ source activate lcdb-wf-test
+
+ # rsync is required for the deployment process
+ apt install -y rsync
+
+ # Deploy to the new directory, so we are testing the real-world case of post-deployment.
+ # Note that $DEPLOY is set in the "set-paths" step configured above.
+ python deploy.py --flavor full --dest $DEPLOY --branch $GITHUB_HEAD_REF --clone
+
+ # Separately copy over some test-specific files
+ cp workflows/chipseq/run_test.sh $DEPLOY/workflows/chipseq
+ cp workflows/rnaseq/run_test.sh $DEPLOY/workflows/rnaseq
+ cp workflows/rnaseq/run_downstream_test.sh $DEPLOY/workflows/rnaseq
+ cp workflows/colocalization/run_test.sh $DEPLOY/workflows/references
+ cp workflows/colocalization/run_test.sh $DEPLOY/workflows/colocalization
+ mkdir $DEPLOY/ci
+ mkdir $DEPLOY/test
+ cp test/lcdb-wf-test $DEPLOY/test
+ cp test/workflow_test_params.yaml $DEPLOY/test
+ cp ci/get-data.py $DEPLOY/ci
+
+ # the ./run_test.sh scripts run this
+ cp ci/preprocessor.py $DEPLOY/ci
+
+ # download example data
+ cd $DEPLOY
+ test/lcdb-wf-test data --kind=all --verbose
+
+ - name: chipseq misc
run: |
+ cd $DEPLOY/workflows/chipseq
source activate lcdb-wf-test
- STAR --version
+ ./run_test.sh --use-conda -j2 -k -p -r \
+ --configfile $ORIG/test/test_configs/test_chipseq_regression.yaml \
+ --config sampletable=$ORIG/test/test_configs/chipseq_one_run.tsv \
+ merged_bigwigs="{}" \
+ --until bed_to_bigbed
From 8ceaf5abfcc63f92350cde4e631bdd044a2b2ac0 Mon Sep 17 00:00:00 2001
From: daler <ryan.dale@nih.gov>
Date: Sun, 2 Apr 2023 11:15:51 -0400
Subject: [PATCH 91/91] syntax
---
.github/workflows/main.yaml | 46 ++++++++++++++++++-------------------
1 file changed, 23 insertions(+), 23 deletions(-)
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
index 058e9590..f8a41faf 100644
--- a/.github/workflows/main.yaml
+++ b/.github/workflows/main.yaml
@@ -38,34 +38,34 @@ jobs:
- name: Download example data
run: |
- conda info --envs
- source activate lcdb-wf-test
+ conda info --envs
+ source activate lcdb-wf-test
- # rsync is required for the deployment process
- apt install -y rsync
+ # rsync is required for the deployment process
+ apt install -y rsync
- # Deploy to the new directory, so we are testing the real-world case of post-deployment.
- # Note that $DEPLOY is set in the "set-paths" step configured above.
- python deploy.py --flavor full --dest $DEPLOY --branch $GITHUB_HEAD_REF --clone
+ # Deploy to the new directory, so we are testing the real-world case of post-deployment.
+ # Note that $DEPLOY is set in the "set-paths" step configured above.
+ python deploy.py --flavor full --dest $DEPLOY --branch $GITHUB_HEAD_REF --clone
- # Separately copy over some test-specific files
- cp workflows/chipseq/run_test.sh $DEPLOY/workflows/chipseq
- cp workflows/rnaseq/run_test.sh $DEPLOY/workflows/rnaseq
- cp workflows/rnaseq/run_downstream_test.sh $DEPLOY/workflows/rnaseq
- cp workflows/colocalization/run_test.sh $DEPLOY/workflows/references
- cp workflows/colocalization/run_test.sh $DEPLOY/workflows/colocalization
- mkdir $DEPLOY/ci
- mkdir $DEPLOY/test
- cp test/lcdb-wf-test $DEPLOY/test
- cp test/workflow_test_params.yaml $DEPLOY/test
- cp ci/get-data.py $DEPLOY/ci
+ # Separately copy over some test-specific files
+ cp workflows/chipseq/run_test.sh $DEPLOY/workflows/chipseq
+ cp workflows/rnaseq/run_test.sh $DEPLOY/workflows/rnaseq
+ cp workflows/rnaseq/run_downstream_test.sh $DEPLOY/workflows/rnaseq
+ cp workflows/colocalization/run_test.sh $DEPLOY/workflows/references
+ cp workflows/colocalization/run_test.sh $DEPLOY/workflows/colocalization
+ mkdir $DEPLOY/ci
+ mkdir $DEPLOY/test
+ cp test/lcdb-wf-test $DEPLOY/test
+ cp test/workflow_test_params.yaml $DEPLOY/test
+ cp ci/get-data.py $DEPLOY/ci
- # the ./run_test.sh scripts run this
- cp ci/preprocessor.py $DEPLOY/ci
+ # the ./run_test.sh scripts run this
+ cp ci/preprocessor.py $DEPLOY/ci
- # download example data
- cd $DEPLOY
- test/lcdb-wf-test data --kind=all --verbose
+ # download example data
+ cd $DEPLOY
+ test/lcdb-wf-test data --kind=all --verbose
- name: chipseq misc
run: |