From acd04bf8da7ee1da4847981e27a26ca33be14982 Mon Sep 17 00:00:00 2001 From: Lukas Heumos Date: Mon, 25 Apr 2022 13:19:32 +0200 Subject: [PATCH 1/9] Add packages for tools chapter --- python-packages.txt | 3 +++ 1 file changed, 3 insertions(+) diff --git a/python-packages.txt b/python-packages.txt index 04a4c2a..c61063c 100644 --- a/python-packages.txt +++ b/python-packages.txt @@ -19,4 +19,7 @@ episcanpy cellrank #cellrank[krylov] sfaira +mudatasets +pysam +scvi-tools pandas==1.2.5 From a1a211f3f607fb970725500a7d26ad4841f4fe54 Mon Sep 17 00:00:00 2001 From: Lukas Heumos Date: Mon, 25 Apr 2022 13:59:50 +0200 Subject: [PATCH 2/9] Add muon & mudata --- python-packages.txt | 2 ++ 1 file changed, 2 insertions(+) diff --git a/python-packages.txt b/python-packages.txt index c61063c..57ec9ee 100644 --- a/python-packages.txt +++ b/python-packages.txt @@ -19,6 +19,8 @@ episcanpy cellrank #cellrank[krylov] sfaira +muon +mudata mudatasets pysam scvi-tools From f98f5f83c7c35801b4ecdc809da901e6fe983f2b Mon Sep 17 00:00:00 2001 From: Lukas Heumos Date: Mon, 25 Apr 2022 22:43:11 +0200 Subject: [PATCH 3/9] remove pysam --- python-packages.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/python-packages.txt b/python-packages.txt index 57ec9ee..c726e77 100644 --- a/python-packages.txt +++ b/python-packages.txt @@ -22,6 +22,5 @@ sfaira muon mudata mudatasets -pysam scvi-tools pandas==1.2.5 From 53b66e3054bcd3daaaca9fe68154419b86160b53 Mon Sep 17 00:00:00 2001 From: Lukas Heumos Date: Tue, 26 Apr 2022 09:19:39 +0200 Subject: [PATCH 4/9] Use pip legacy resolver --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index e814992..196aeb0 100644 --- a/Dockerfile +++ b/Dockerfile @@ -12,7 +12,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends htop less nano # Install python packages COPY python-packages.txt /opt/python/python-packages.txt RUN pip install --no-cache-dir -U pip wheel setuptools==57.5 cmake -RUN pip install --no-cache-dir -r /opt/python/python-packages.txt +RUN pip install --no-cache-dir --use-deprecated=legacy-resolver -r /opt/python/python-packages.txt RUN jupyter contrib nbextension install --system RUN jupyter nbextension enable --py widgetsnbextension From b403c8e5a9ff52853986cdd9225d9c9a7db973c2 Mon Sep 17 00:00:00 2001 From: Leander <20015434+le-ander@users.noreply.github.com> Date: Tue, 26 Apr 2022 09:56:39 +0200 Subject: [PATCH 5/9] Fix R version more thoroughly --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 196aeb0..f49072d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -24,7 +24,7 @@ RUN jupyter labextension install @aquirdturtle/collapsible_headings @jupyterlab/ # Install R and packages (precompiled if possible) RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-key '95C0FAF38DB3CCAD0C080A7BDC78B2DDEABC47B7' RUN echo "deb http://cloud.r-project.org/bin/linux/debian bullseye-cran40/" | tee -a /etc/apt/sources.list -RUN apt-get update && apt-get install -y --no-install-recommends r-base-dev=4.1.2-1~bullseyecran.0 +RUN apt-get update && apt-get install -y --no-install-recommends r-base-core=4.1.2-1~bullseyecran.0 r-base-dev=4.1.2-1~bullseyecran.0 RUN apt-get install -y --no-install-recommends r-cran-devtools r-cran-gam r-cran-rcolorbrewer r-cran-biocmanager r-cran-irkernel RUN apt-get install -y --no-install-recommends r-bioc-scran r-bioc-monocle r-bioc-complexheatmap r-bioc-limma r-bioc-dropletutils RUN Rscript -e "BiocManager::install(c('MAST','slingshot','clusterExperiment'), version = '3.14')" From aa565d6e7a252e39eda155874c18cebdbc8f0731 Mon Sep 17 00:00:00 2001 From: Leander <20015434+le-ander@users.noreply.github.com> Date: Tue, 26 Apr 2022 10:01:28 +0200 Subject: [PATCH 6/9] Add lme4 R package Required for fitting random effect models in MAST --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index f49072d..b6065fb 100644 --- a/Dockerfile +++ b/Dockerfile @@ -25,7 +25,7 @@ RUN jupyter labextension install @aquirdturtle/collapsible_headings @jupyterlab/ RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-key '95C0FAF38DB3CCAD0C080A7BDC78B2DDEABC47B7' RUN echo "deb http://cloud.r-project.org/bin/linux/debian bullseye-cran40/" | tee -a /etc/apt/sources.list RUN apt-get update && apt-get install -y --no-install-recommends r-base-core=4.1.2-1~bullseyecran.0 r-base-dev=4.1.2-1~bullseyecran.0 -RUN apt-get install -y --no-install-recommends r-cran-devtools r-cran-gam r-cran-rcolorbrewer r-cran-biocmanager r-cran-irkernel +RUN apt-get install -y --no-install-recommends r-cran-devtools r-cran-gam r-cran-rcolorbrewer r-cran-biocmanager r-cran-irkernel r-cran-lme4 RUN apt-get install -y --no-install-recommends r-bioc-scran r-bioc-monocle r-bioc-complexheatmap r-bioc-limma r-bioc-dropletutils RUN Rscript -e "BiocManager::install(c('MAST','slingshot','clusterExperiment'), version = '3.14')" RUN Rscript -e 'writeLines(capture.output(sessionInfo()), "../package_versions_r.txt")' --default-packages=scran,RColorBrewer,slingshot,monocle,gam,clusterExperiment,ggplot2,plyr,MAST,DropletUtils,IRkernel From e8b9de0bd6344df3e7c7ed4bce6a73dce083ce44 Mon Sep 17 00:00:00 2001 From: Leander <20015434+le-ander@users.noreply.github.com> Date: Tue, 26 Apr 2022 10:45:37 +0200 Subject: [PATCH 7/9] Manually hold R version using apt-mark --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index b6065fb..cda2091 100644 --- a/Dockerfile +++ b/Dockerfile @@ -25,6 +25,7 @@ RUN jupyter labextension install @aquirdturtle/collapsible_headings @jupyterlab/ RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-key '95C0FAF38DB3CCAD0C080A7BDC78B2DDEABC47B7' RUN echo "deb http://cloud.r-project.org/bin/linux/debian bullseye-cran40/" | tee -a /etc/apt/sources.list RUN apt-get update && apt-get install -y --no-install-recommends r-base-core=4.1.2-1~bullseyecran.0 r-base-dev=4.1.2-1~bullseyecran.0 +RUN apt-mark hold r-base-core RUN apt-get install -y --no-install-recommends r-cran-devtools r-cran-gam r-cran-rcolorbrewer r-cran-biocmanager r-cran-irkernel r-cran-lme4 RUN apt-get install -y --no-install-recommends r-bioc-scran r-bioc-monocle r-bioc-complexheatmap r-bioc-limma r-bioc-dropletutils RUN Rscript -e "BiocManager::install(c('MAST','slingshot','clusterExperiment'), version = '3.14')" From f520e3080d1f6511a930dd9f8422c8e9e4f17c34 Mon Sep 17 00:00:00 2001 From: Leander <20015434+le-ander@users.noreply.github.com> Date: Tue, 26 Apr 2022 11:00:54 +0200 Subject: [PATCH 8/9] Remove pinning of R and bioc versions R version pinning does not work when installing R packages with apt. --- Dockerfile | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index cda2091..b76382a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -24,11 +24,10 @@ RUN jupyter labextension install @aquirdturtle/collapsible_headings @jupyterlab/ # Install R and packages (precompiled if possible) RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-key '95C0FAF38DB3CCAD0C080A7BDC78B2DDEABC47B7' RUN echo "deb http://cloud.r-project.org/bin/linux/debian bullseye-cran40/" | tee -a /etc/apt/sources.list -RUN apt-get update && apt-get install -y --no-install-recommends r-base-core=4.1.2-1~bullseyecran.0 r-base-dev=4.1.2-1~bullseyecran.0 -RUN apt-mark hold r-base-core +RUN apt-get update && apt-get install -y --no-install-recommends r-base-dev RUN apt-get install -y --no-install-recommends r-cran-devtools r-cran-gam r-cran-rcolorbrewer r-cran-biocmanager r-cran-irkernel r-cran-lme4 RUN apt-get install -y --no-install-recommends r-bioc-scran r-bioc-monocle r-bioc-complexheatmap r-bioc-limma r-bioc-dropletutils -RUN Rscript -e "BiocManager::install(c('MAST','slingshot','clusterExperiment'), version = '3.14')" +RUN Rscript -e "BiocManager::install(c('MAST','slingshot','clusterExperiment'))" RUN Rscript -e 'writeLines(capture.output(sessionInfo()), "../package_versions_r.txt")' --default-packages=scran,RColorBrewer,slingshot,monocle,gam,clusterExperiment,ggplot2,plyr,MAST,DropletUtils,IRkernel # Install python-R interoperability packages From d769fda186cfa4f82d540a1f397717adb143b2d3 Mon Sep 17 00:00:00 2001 From: Leander <20015434+le-ander@users.noreply.github.com> Date: Tue, 26 Apr 2022 11:58:51 +0200 Subject: [PATCH 9/9] Use PyVCF3 insttead of PyVCF PyVCF is no longer maintained and incompatible with setuptools 58 and newer --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index b76382a..7aee570 100644 --- a/Dockerfile +++ b/Dockerfile @@ -44,7 +44,7 @@ RUN apt-get install -y --no-install-recommends r-bioc-edger # Fabi's section RUN apt-get install -y --no-install-recommends freebayes parallel libhts-dev -RUN pip install --no-cache-dir -U pegasuspy vireoSNP PyVCF scSplit +RUN pip install --no-cache-dir -U pegasuspy vireoSNP PyVCF3 scSplit RUN apt-get install -y --no-install-recommends r-cran-seurat ## cellsnp-lite (requires htslib) WORKDIR /opt/cellsnp