![\"Version\"](\"https://img.shields.io/github/tag/maplesond/portcullis.svg\"\)
\n![\"License:](\"https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg\"\){kind=icon}
\n![\"Issues\"](\"https://img.shields.io/github/issues-raw/maplesond/portcullis.svg\"\)
\n
Portcullis stands for PORTable CULLing\ \ of Invalid Splice junctions from pre-aligned RNA-seq data. It is known that\ @@ -17931,7 +17931,7 @@ EI-CoreBioinformatics/portcullis: \ for installing and running portcullis. Hopefully your favourite container or\ \ package manager is supported below. If not let us know and we'll try to work\ \ to get it integrated there.
\nDocker
\n![\"Docker](\"https://img.shields.io/docker/pulls/maplesond/portcullis.svg\"\)
# Keep in mind you need to mount\
\ in any working directories to the container with the `-v` option.\n# Ideally,\
@@ -17941,18 +17941,18 @@ EI-CoreBioinformatics/portcullis:
\ First download the container:\nsingularity pull --name portcullis.img shub://maplesond/portcullis:master\n\
\n# Then to execute commands in the container:\nsingularity exec portcullis.img\
\ portcullis --help\nConda
\n![\"Anaconda-Server](\"https://anaconda.org/bioconda/portcullis/badges/latest_release_date.svg\"\)
![\"Anaconda-Server](\"https://anaconda.org/bioconda/portcullis/badges/platforms.svg\"\)
![\"Anaconda-Server](\"https://anaconda.org/bioconda/portcullis/badges/downloads.svg\"\)
conda install portcullis --channel=bioconda\n\
Brew
\nbrew install brewsci/bio/portcullis\n\
From source
\nIf you wish to install from source please\ \ first confirm that first you have these dependencies are installed and configured:
\n\ @@ -18016,7 +18016,7 @@ EI-CoreBioinformatics/portcullis: -1\" href=\"#acknowledgements\">Acknowledgements\nAffiliation: The Earlham Institute (EI)\n\ Funding: The Biotechnology and Biological Sciences Research Council (BBSRC)
\n" - stargazers_count: 32 + stargazers_count: 33 subscribers_count: 5 topics: - portcullis @@ -18024,7 +18024,7 @@ EI-CoreBioinformatics/portcullis: - splice-junctions - bam-files - filter - updated_at: 1693233930.0 + updated_at: 1702669138.0 EPI-APE/simu_IV: data_format: 2 description: null @@ -19378,63 +19378,67 @@ Gaius-Augustus/Augustus: readme: "![\"Build](\"https://github.com/Gaius-Augustus/Augustus/workflows/Build%20and%20test/badge.svg\"\){kind=icon}
INTRODUCTION
\nINSTALLATION
\n\
- RUNNING AUGUSTUS
\nWEB-SERVER
\nCOMPARATIVE GENE PREDICTION
\n\
- AUTHORS AND CONTACT
\nREFERENCES
\nLICENSES
AUGUSTUS is a program\ - \ to find genes and their structures in one or more genomes. More ...
\nWindows users can use the Windows Subsystem\ - \ for Linux (WSL) to install AUGUSTUS exactly as described below for Linux. How\ - \ to set up the WSL for AUGUSTUS is described here.
\nINTRODUCTION
\nINSTALLATION
\nRUNNING\
+ \ AUGUSTUS
\nWEB-SERVER
\nCOMPARATIVE GENE PREDICTION
\nAUTHORS AND\
+ \ CONTACT
\nREFERENCES
\n\
+ LICENSES
AUGUSTUS is a program to find genes and their structures in one or more genomes.\ + \ More ...
\nWindows users can use the Windows Subsystem for Linux\ + \ (WSL) to install AUGUSTUS exactly as described below for Linux. How to set up\ + \ the WSL for AUGUSTUS is described here.
\n\ +Until Ubuntu 21.04 and Debian 11 only as single-genome version, since then\ \ with capability for comparative gene prediction.
\n![\"Downloads\"](\"https://img.shields.io/github/downloads/maplesond/portcullis/total.svg\"\)
![\"GitHub](\"https://img.shields.io/github/downloads/gaius-augustus/augustus/total\"\)
sudo apt install\
- \ augustus augustus-data augustus-doc\nCreate a docker image from Dockerfile using:
\ngit clone https://github.com/Gaius-Augustus/Augustus.git\n\
- cd Augustus\ndocker build -t augustus .\nCreate a Singularity\ - \ Image File from the Singularity Definition File\ - \ using
\ngit clone https://github.com/Gaius-Augustus/Augustus.git\n\
- cd Augustus\nsingularity build augustus.sif Singularity.def\nSee INSTALL.md for details.
\nDownload source code from github and compile:
\n\ + \ augustus augustus-data augustus-doc\n\nCreate a docker image from Dockerfile using:
\n\git clone https://github.com/Gaius-Augustus/Augustus.git\ncd Augustus\n\
- make augustus\nAfter compilation has finished, the command bin/augustus\ - \ should be executable and print a usage message.
\nFor utilities use
\n\ -make auxprogs\nAs a normal user, add\ - \ the directory of the executables to the PATH environment variable, for example:
\n\ -export PATH=~/augustus/bin:~/augustus/scripts:$PATH\nYou can install AUGUSTUS globally, if you have root privileges, for example:
\n\ -sudo make install\nAlternatively, you can exectue\ - \ similar commands to those in the \"install\" section of the top-level Makefile\ - \ to customize the global installation.
\nIf the environment variable\ + docker build -t augustus .\n\n
Create a Singularity Image File from the Singularity\ + \ Definition File using
\ngit clone https://github.com/Gaius-Augustus/Augustus.git\n\
+ cd Augustus\nsingularity build augustus.sif Singularity.def\nSee INSTALL.md for details.
\nDownload\ + \ source code from github and compile:
\ngit clone https://github.com/Gaius-Augustus/Augustus.git\n\
+ cd Augustus\nmake augustus\nAfter compilation has finished,\ + \ the command bin/augustus should be executable and print a usage message.
\n\ +For utilities use
\nmake auxprogs\nAs a normal user, add the directory of the\ + \ executables to the PATH environment variable, for example:
\nexport\
+ \ PATH=~/augustus/bin:~/augustus/scripts:$PATH\nYou can install AUGUSTUS globally, if you have root privileges,\ + \ for example:
\nsudo make install\nAlternatively,\ + \ you can exectue similar commands to those in the \"install\" section of the\ + \ top-level Makefile to customize the global installation.
\nIf the environment variable\ \ AUGUSTUS_CONFIG_PATH is set, augustus and etraining will look there for the\ \ config directory that contains the configuration and parameter files, e.g. '~/augustus/config'.\ \ You may want to add this line to a startup script (like ~/.bashrc).
\nexport\
@@ -19443,38 +19447,39 @@ Gaius-Augustus/Augustus:
\ path ../config relative to the directory in which the executable lies. As a\
\ third alternative, you can specify this directory on the command line when you\
\ run augustus:\n--AUGUSTUS_CONFIG_PATH=/my_path_to_AUGUSTUS/augustus/config/\n\
- WEB-SERVER
\n\
- AUGUSTUS can also be run through a web-interface at http://bioinf.uni-greifswald.de/augustus/ and a web service\
- \ at http://bioinf.uni-greifswald.de/webaugustus/.
\nREFERENCES AND\
- \ DOCUMENTATION
\n\
+ WEB-SERVER
\nAUGUSTUS can also be run through a web-interface\
+ \ at http://bioinf.uni-greifswald.de/augustus/\
+ \ and a web service at http://bioinf.uni-greifswald.de/webaugustus/.
\nREFERENCES AND DOCUMENTATION
\n\
Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008).\nUsing native and syntenically mapped cDNA alignments to improve de novo gene\
\ finding. Bioinformatics, 24(5), pages 637\u2013644, doi: 10.1093/bioinformatics/btn013
\n\
For further references see docs/REFERENCES.md
\n\
3 book chapters with command line walkthroughs
\nLICENSESAll\
- \ source code, i.e.
\n\n- the AUGUSTUS source code (
src/*.cc,\
- \ include/*.hh) \n- the scripts (
scripts/*) \n\
- - the auxiliary programs (
auxprogs/) \n- the tree-parser\
- \ (
src/scanner, src/parser) \n- the unit tests\
- \ (
src/unittests) \n
\nis under the Artistic License.
\n"
- stargazers_count: 232
- subscribers_count: 18
+ \ rel=\"nofollow\">3 book chapters with command line walkthroughs\nLICENSES
\nAll source code, i.e.
\n\n- the AUGUSTUS\
+ \ source code (
src/*.cc, include/*.hh) \n- the\
+ \ scripts (
scripts/*) \n- the auxiliary programs (
auxprogs/) \n\
+ - the tree-parser (
src/scanner, src/parser) \n\
+ - the unit tests (
src/unittests) \n
\nis under the Artistic License.
\n"
+ stargazers_count: 244
+ subscribers_count: 19
topics:
- genome
- annotation
- gene
- prediction
- discovery
- updated_at: 1696433872.0
+ updated_at: 1705653648.0
Gaoyuan-Liu/Non-prehensile-Augmented-TAMP:
data_format: 2
description: null
@@ -19968,9 +19973,10 @@ GoHypernet/Galileo-examples:
- hpcc/Singularityfile
full_name: GoHypernet/Galileo-examples
latest_release: null
- readme: 'Galileo application example repository
+ readme: 'Galileo application
+ example repository
This repository contains a number of examples, representing many frameworks,
@@ -27618,7 +27624,7 @@ IARCbioinfo/mutect-nf:
'
stargazers_count: 9
- subscribers_count: 4
+ subscribers_count: 5
topics:
- nextflow
- mutect
@@ -38604,7 +38610,7 @@ MPIB/singularity-ants:
tabindex="-1" href="#singularity-ants">singularity-ants
-
@@ -38868,7 +38874,7 @@ MPIB/singularity-mrtrix3:
tabindex="-1" href="#singularity-mrtrix3">singularity-mrtrix3
-
@@ -39009,7 +39015,7 @@ MRChemSoft/mrchem:
- recipes/Singularity.openmpi4.0
- recipes/Singularity.nompi
full_name: MRChemSoft/mrchem
- latest_release: v1.1.3
+ latest_release: v1.1.4
readme: "![\"MRChem](\"https://github.com/MRChemSoft/mrchem/raw/master/doc/gfx/logo_full.png\"\)
\nThank you for your interest\
\ in contributing to MRtrix3! Please read on here to find out how to report issues, request features and make direct contributions.
\n"
- stargazers_count: 263
+ stargazers_count: 266
subscribers_count: 32
topics: []
- updated_at: 1705148089.0
+ updated_at: 1705636513.0
MacIver-Lab/Ergodic-Information-Harvesting:
data_format: 2
description: 'Code, data, and tutorials for "Sense organ control in moths to moles
@@ -40627,17 +40633,17 @@ MicroSTM/singularity_containers:
data_format: 2
description: Singularity containers
filenames:
- - Singularity.py35_mcts
- - Singularity.py37_pybullet~
- - Singularity.py36_pybullet_pybox2d_pytorch
- Singularity.py37_pybullet
+ - Singularity.py37_mcts
+ - Singularity.py35_mcts
- Singularity.py37_mcts~
- Singularity.py35
- - Singularity.py37_mcts
+ - Singularity.py36_pybullet_pybox2d_pytorch
+ - Singularity.py37_pybullet~
full_name: MicroSTM/singularity_containers
latest_release: null
- readme: 'singularity
+ readme: 'singularity
Singularity containers
@@ -42239,8 +42245,8 @@ MuhsinFatih/singularityimages:
data_format: 2
description: null
filenames:
- - Singularity.tensorflow-1.14
- Singularity.tensorflow_venv
+ - Singularity.tensorflow-1.14
full_name: MuhsinFatih/singularityimages
latest_release: null
stargazers_count: 0
@@ -43949,14 +43955,14 @@ NOAA-GFDL/AM4:
NOAA-GFDL at https://gitlab.gfdl.noaa.gov.
'
- stargazers_count: 17
+ stargazers_count: 18
subscribers_count: 8
topics:
- fortran
- jupyter-notebook
- shell-script
- ncl
- updated_at: 1699456573.0
+ updated_at: 1705669583.0
NOAA-GFDL/CM4:
data_format: 2
description: null
@@ -50676,7 +50682,7 @@ PawseySC/containers-openfoam-workshop-scripts:
full_name: PawseySC/containers-openfoam-workshop-scripts
latest_release: null
readme: 'Workshop on the usage
of OpenFOAM containers at Pawsey
@@ -51714,10 +51720,10 @@ QTIM-Lab/DeepNeuro:
octicon octicon-link\">Disclaimer\nThis software package and\
\ the deep learning models within are intended for research purposes only and\
\ have not yet been validated for clinical use.
\n"
- stargazers_count: 118
+ stargazers_count: 120
subscribers_count: 14
topics: []
- updated_at: 1703042625.0
+ updated_at: 1704941505.0
QsingularityAi/polar-pfc-master_active-crystel:
data_format: 2
description: null
@@ -52310,6 +52316,7 @@ ReproNim/containers:
- images/bids/Singularity.bids-micapipe--0.0.1
- images/bids/Singularity.bids-qsiprep--0.18.1
- images/bids/Singularity.bids-pymvpa--4.0.1
+ - images/bids/Singularity.bids-qsiprep--0.20.0
- images/bids/Singularity.bids-qsiprep--0.16.0RC3
- images/bids/Singularity.bids-xcp-d--0.6.0
- images/bids/Singularity.bids-rshrf--1.0.1
@@ -53351,10 +53358,10 @@ ReproNim/sfn2018-training:
data_format: 2
description: Materials for SfN 2018 training event
filenames:
- - section23/environments/Singularity.heudiconvn
- section23/environments/Singularity.fsl
- - section23/environments/Singularity.fsln
+ - section23/environments/Singularity.heudiconvn
- section23/environments/Singularity.heudiconv
+ - section23/environments/Singularity.fsln
full_name: ReproNim/sfn2018-training
latest_release: null
readme: '
Phigaro is a standalone command-line\ \ application that is able to detect prophage regions taking raw genome and metagenome\ @@ -79392,7 +79397,7 @@ bobeobibo/phigaro:
(c) E.Starikova, P. Tikhonova,\ \ N.Pryanichnikov, 2019
\n" - stargazers_count: 42 + stargazers_count: 43 subscribers_count: 4 topics: - bioinformatics @@ -79406,7 +79411,7 @@ bobeobibo/phigaro: - genomics - genomic-data-analysis - genomic-regions - updated_at: 1693551539.0 + updated_at: 1704738574.0 bow/crimson: data_format: 2 description: Bioinformatics tool outputs converter to JSON or YAML @@ -79749,8 +79754,8 @@ brevans/agalma: description: Singularity definitions for agalma filenames: - Singularity.latest - - versions/Singularity.1.0.0 - versions/Singularity.1.0.1 + - versions/Singularity.1.0.0 full_name: brevans/agalma latest_release: null readme: 'by circulosmeos
\n" - stargazers_count: 922 + stargazers_count: 925 subscribers_count: 20 topics: - perl-scripts @@ -82469,7 +82474,7 @@ circulosmeos/gdown.pl: - wget - gdrive - dockerfile - updated_at: 1701439860.0 + updated_at: 1705471917.0 cjknight/singularity_test: data_format: 2 description: null @@ -84059,129 +84064,137 @@ cokelaer/damona: description: singularity environment manager (application to NGS and bioinformatics) filenames: - test/data/Singularity.testing_1.0.0 - - damona/software/polypolish/Singularity.polypolish_0.5.0 - - damona/software/multiqc/Singularity.multiqc_1.16.0 - - damona/software/bbtools/Singularity.bbtools_38.94.0 - damona/software/trinity/Singularity.trinity_2.15.1 - - damona/software/raxml/Singularity.raxml_8.2.12 + - damona/software/pbbam/Singularity.pbbam_2.1.0 + - damona/software/pbbam/Singularity.pbbam_2.3.0 + - damona/software/sequana_perl_tools/Singularity.sequana_perl_tools_0.2.0 + - damona/software/sequana_perl_tools/Singularity.sequana_perl_tools_0.1.0 + - damona/software/seqtk/Singularity.seqtk_1.3.0 + - damona/software/transdecoder/Singularity.trandecoder_5.7.0 + - damona/software/quast/Singularity.quast_5.2.0 + - damona/software/quast/Singularity.quast_5.0.2 + - damona/software/rnaseqc/Singularity.rnaseqc_2.35.0 + - damona/software/rtools/Singularity.rtools_1.1.0 + - damona/software/rtools/Singularity.rtools_1.2.0 + - damona/software/rtools/Singularity.rtools_1.0.0 + - damona/software/vt/Singularity.vt_0.57721.0 + - damona/software/bcl2fastq/Singularity.bcl2fastq_2.20.0 + - damona/software/ccs/Singularity.ccs_6.4.0 + - damona/software/gzip/Singularity.gzip_1.9.0 - damona/software/bowtie/Singularity.bowtie_1.3.1 - - damona/software/gffread/Singularity.gffread_0.12.1 - - damona/software/gffread/Singularity.gffread_0.12.7 - - damona/software/pigz/Singularity.pigz_2.4.0 - - damona/software/igvtools/Singularity.igvtools_2.12.0 - - damona/software/trf/Singularity.trf_4.10.0 - - damona/software/samtools/Singularity.samtools_1.16.1 - - damona/software/samtools/Singularity.samtools_1.15.0 - - damona/software/pycoqc/Singularity.pycoqc_2.5.2 - - damona/software/fastp/Singularity.fastp_0.23.3 - - damona/software/fastp/Singularity.fastp_0.23.2 - damona/software/samtools_minimap2/Singularity.samtools_1.17_minimap2_2.24.0 + - damona/software/phantompeakqualtools/Singularity.phantompeakqualtools_1.2.2 + - damona/software/flye/Singularity.flye_2.9.3 + - damona/software/flye/Singularity.flye_2.9.1 + - damona/software/flye/Singularity.flye_2.9.0 + - damona/software/flye/Singularity.flye_2.9.2 + - damona/software/bedtools/Singularity.bedtools_2.30.0 - damona/software/canu/Singularity.canu_2.1.1 - damona/software/canu/Singularity.canu_1.8.0 - damona/software/canu/Singularity.canu_1.6.0 - - damona/software/art/Singularity.art_2.5.8 - - damona/software/art/Singularity.art_3.11.14 - - damona/software/bcl2fastq/Singularity.bcl2fastq_2.20.0 - - damona/software/bedtools/Singularity.bedtools_2.30.0 - - damona/software/rtools/Singularity.rtools_1.2.0 - - damona/software/rtools/Singularity.rtools_1.0.0 - - damona/software/rtools/Singularity.rtools_1.1.0 - - damona/software/circlator/Singularity.circlator_1.5.5 - - damona/software/pbbam/Singularity.pbbam_2.3.0 - - damona/software/pbbam/Singularity.pbbam_2.1.0 - - damona/software/jellyfish/Singularity.jellyfish_2.3.0 - - damona/software/trinotate/Singularity.trinotate_4.0.1 - - damona/software/flye/Singularity.flye_2.9.0 - - damona/software/flye/Singularity.flye_2.9.1 - - damona/software/checkm/Singularity.checkm_1.2.2 - - damona/software/hmmer/Singularity.hmmer_3.3.2 - - damona/software/vt/Singularity.vt_0.57721.0 - - damona/software/kraken/Singularity.kraken_2.0.9 - - damona/software/kraken/Singularity.kraken_1.1.0 + - damona/software/subread/Singularity.subread_2.0.3 + - damona/software/multiqc/Singularity.multiqc_1.16.0 + - damona/software/trim_galore/Singularity.trimgalore_0.5.0 + - damona/software/samtools/Singularity.samtools_1.16.1 + - damona/software/samtools/Singularity.samtools_1.15.0 - damona/software/snpeff/Singularity.snpeff_5.0.0 - damona/software/snpeff/Singularity.snpeff_5.1.0 - - damona/software/graphviz/Singularity.graphviz_7.0.5 - - damona/software/graphviz/Singularity.graphviz_2.43.0 - - damona/software/pplacer/Singularity.pplacer_1.1.0 - - damona/software/salmon/Singularity.salmon_1.3.0 - - damona/software/falco/Singularity.falco_0.2.1 - - damona/software/falco/Singularity.falco_1.0.0 - - damona/software/mafft/Singularity.mafft_7.520.0 - - damona/software/seacr/Singularity.seacr_1.3.0 + - damona/software/bamtools/Singularity.bamtools_2.5.2 - damona/software/cellranger_atac/Singularity.cellranger_atac_2.1.0 - - damona/software/rnaseqc/Singularity.rnaseqc_2.35.0 - - damona/software/busco/Singularity.busco_5.4.6 - - damona/software/blast/Singularity.blast_2.12.0 - - damona/software/hifiasm/Singularity.hifiasm_0.19.1 - - damona/software/pangolin/Singularity.pangolin_4.3.0 - - damona/software/sequana_denovo/Singularity.sequana_denovo_0.0.2 - - damona/software/bowtie2/Singularity.bowtie2_2.3.4 - - damona/software/bowtie2/Singularity.bowtie2_2.4.2 - - damona/software/bowtie2/Singularity.bowtie2_2.5.1 - - damona/software/ucsc/Singularity.ucsc_3.7.7 - - damona/software/prokka/Singularity.prokka_1.14.5 - - damona/software/prokka/Singularity.prokka_1.14.6 - - damona/software/bioconvert/Singularity.bioconvert_0.6.3 - - damona/software/bioconvert/Singularity.bioconvert_0.6.1 - - damona/software/bioconvert/Singularity.bioconvert_0.6.2 - - damona/software/bioconvert/Singularity.bioconvert_1.0.0 - - damona/software/bioconvert/Singularity.bioconvert_1.1.0 - damona/software/homer/Singularity.homer_4.11.0 - - damona/software/nextclade/Singularity.nextclade_2.15.0 - - damona/software/idr/Singularity.idr_2.0.3 - - damona/software/sequana/Singularity.sequana_0.15.0 - - damona/software/sequana/Singularity.sequana_0.12.6 - - damona/software/sequana/Singularity.sequana_0.14.6 - - damona/software/sequana/Singularity.sequana_0.16.1 - - damona/software/bwa/Singularity.bwa_0.7.17 - - damona/software/fastqc/Singularity.fastqc_0.11.9_py3 + - damona/software/medaka/Singularity.medaka_1.7.3 + - damona/software/nanopolish/Singularity.nanopolish_0.14.0 + - damona/software/pplacer/Singularity.pplacer_1.1.0 - damona/software/fastqc/Singularity.fastqc_0.11.9 - - damona/software/fastqc/Singularity.fastqc_0.11.8 - damona/software/fastqc/Singularity.fastqc_0.12.1 - - damona/software/ivar/Singularity.ivar_1.3.1 - - damona/software/rnadiff/Singularity.rnadiff_1.7.1 - - damona/software/sequana_tools/Singularity.sequana_tools_0.9.0 + - damona/software/fastqc/Singularity.fastqc_0.11.9_py3 + - damona/software/fastqc/Singularity.fastqc_0.11.8 + - damona/software/pigz/Singularity.pigz_2.4.0 + - damona/software/blast/Singularity.blast_2.12.0 + - damona/software/cd-hit/Singularity.cd-hit_4.8.1 + - damona/software/raxml/Singularity.raxml_8.2.12 + - damona/software/sequana_tools/Singularity.sequana_tools_0.12.0 + - damona/software/sequana_tools/Singularity.sequana_tools_0.14.3 - damona/software/sequana_tools/Singularity.sequana_tools_0.14.2 + - damona/software/sequana_tools/Singularity.sequana_tools_0.14.5 + - damona/software/sequana_tools/Singularity.sequana_tools_0.9.0 + - damona/software/sequana_tools/Singularity.sequana_tools_0.11.0 - damona/software/sequana_tools/Singularity.sequana_tools_0.15.1 - - damona/software/sequana_tools/Singularity.sequana_tools_0.12.0 - damona/software/sequana_tools/Singularity.sequana_tools_0.14.1 - - damona/software/sequana_tools/Singularity.sequana_tools_0.14.5 - damona/software/sequana_tools/Singularity.sequana_tools_0.10.0 - - damona/software/sequana_tools/Singularity.sequana_tools_0.14.3 - - damona/software/sequana_tools/Singularity.sequana_tools_0.11.0 - - damona/software/transdecoder/Singularity.trandecoder_5.7.0 - - damona/software/trim_galore/Singularity.trimgalore_0.5.0 + - damona/software/nextclade/Singularity.nextclade_2.15.0 + - damona/software/bioconvert/Singularity.bioconvert_0.6.3 + - damona/software/bioconvert/Singularity.bioconvert_1.1.0 + - damona/software/bioconvert/Singularity.bioconvert_1.0.0 + - damona/software/bioconvert/Singularity.bioconvert_0.6.1 + - damona/software/bioconvert/Singularity.bioconvert_0.6.2 + - damona/software/mafft/Singularity.mafft_7.520.0 + - damona/software/circlator/Singularity.circlator_1.5.5 + - damona/software/fastp/Singularity.fastp_0.23.2 + - damona/software/fastp/Singularity.fastp_0.23.3 + - damona/software/seqkit/Singularity.seqkit_2.4.0 + - damona/software/seqkit/Singularity.seqkit_2.1.0 + - damona/software/minimap2/Singularity.minimap2_2.24.0 - damona/software/minimap2/Singularity.minimap2_2.17.0 - damona/software/minimap2/Singularity.minimap2_2.23.0 - - damona/software/minimap2/Singularity.minimap2_2.24.0 - - damona/software/subread/Singularity.subread_2.0.3 - - damona/software/nanopolish/Singularity.nanopolish_0.14.0 - - damona/software/gzip/Singularity.gzip_1.9.0 - - damona/software/cd-hit/Singularity.cd-hit_4.8.1 - - damona/software/bamtools/Singularity.bamtools_2.5.2 - - damona/software/medaka/Singularity.medaka_1.7.3 + - damona/software/freebayes/Singularity.freebayes_1.2.0 + - damona/software/freebayes/Singularity.freebayes_1.3.7 + - damona/software/gffread/Singularity.gffread_0.12.1 + - damona/software/gffread/Singularity.gffread_0.12.7 - damona/software/shustring/Singularity.shustring_2.6.0 - - damona/software/helloworld/Singularity.helloworld_1.0.0 + - damona/software/trinotate/Singularity.trinotate_4.0.1 - damona/software/sequana_ribofinder/Singularity.sequana_ribofinder_0.12.0 - - damona/software/seqkit/Singularity.seqkit_2.1.0 - - damona/software/seqkit/Singularity.seqkit_2.4.0 - - damona/software/sequana_perl_tools/Singularity.sequana_perl_tools_0.1.0 - - damona/software/sequana_perl_tools/Singularity.sequana_perl_tools_0.2.0 - - damona/software/phantompeakqualtools/Singularity.phantompeakqualtools_1.2.2 + - damona/software/jellyfish/Singularity.jellyfish_2.3.0 + - damona/software/bbtools/Singularity.bbtools_38.94.0 - damona/software/guppy/Singularity.guppy_6.4.2 - - damona/software/quast/Singularity.quast_5.2.0 - - damona/software/quast/Singularity.quast_5.0.2 - - damona/software/ccs/Singularity.ccs_6.4.0 - - damona/software/seqtk/Singularity.seqtk_1.3.0 - - damona/library/R/Singularity.R_3.6.3 - - damona/library/R/Singularity.R_4.0.2 - - damona/library/micromamba/Singularity.micromamba_1.4.3 + - damona/software/sequana/Singularity.sequana_0.16.5 + - damona/software/sequana/Singularity.sequana_0.15.0 + - damona/software/sequana/Singularity.sequana_0.12.6 + - damona/software/sequana/Singularity.sequana_0.16.1 + - damona/software/sequana/Singularity.sequana_0.16.2 + - damona/software/sequana/Singularity.sequana_0.14.6 + - damona/software/unicycler/Singularity.unicycler_0.5.0 + - damona/software/checkm/Singularity.checkm_1.2.2 + - damona/software/bowtie2/Singularity.bowtie2_2.4.2 + - damona/software/bowtie2/Singularity.bowtie2_2.5.1 + - damona/software/bowtie2/Singularity.bowtie2_2.3.4 + - damona/software/salmon/Singularity.salmon_1.3.0 + - damona/software/falco/Singularity.falco_0.2.1 + - damona/software/falco/Singularity.falco_1.0.0 + - damona/software/prokka/Singularity.prokka_1.14.6 + - damona/software/prokka/Singularity.prokka_1.14.5 + - damona/software/hifiasm/Singularity.hifiasm_0.19.1 + - damona/software/pangolin/Singularity.pangolin_4.3.0 + - damona/software/busco/Singularity.busco_5.4.6 + - damona/software/polypolish/Singularity.polypolish_0.5.0 + - damona/software/bwa/Singularity.bwa_0.7.17 + - damona/software/hmmer/Singularity.hmmer_3.3.2 + - damona/software/art/Singularity.art_3.11.14 + - damona/software/art/Singularity.art_2.5.8 + - damona/software/ucsc/Singularity.ucsc_3.7.7 + - damona/software/rnadiff/Singularity.rnadiff_1.7.1 + - damona/software/idr/Singularity.idr_2.0.3 + - damona/software/sequana_denovo/Singularity.sequana_denovo_0.0.2 + - damona/software/pycoqc/Singularity.pycoqc_2.5.2 + - damona/software/igvtools/Singularity.igvtools_2.12.0 + - damona/software/laa/Singularity.pblaa_2.4.2 + - damona/software/trf/Singularity.trf_4.10.0 + - damona/software/helloworld/Singularity.helloworld_1.0.0 + - damona/software/ivar/Singularity.ivar_1.3.1 + - damona/software/kraken/Singularity.kraken_1.1.0 + - damona/software/kraken/Singularity.kraken_2.0.9 + - damona/software/seacr/Singularity.seacr_1.3.0 + - damona/software/graphviz/Singularity.graphviz_7.0.5 + - damona/software/graphviz/Singularity.graphviz_2.43.0 - damona/library/conda/Singularity.conda_4.9.2 - damona/library/conda/Singularity.conda_4.7.12 + - damona/library/micromamba/Singularity.micromamba_1.4.3 + - damona/library/R/Singularity.R_3.6.3 + - damona/library/R/Singularity.R_4.0.2 full_name: cokelaer/damona - latest_release: v0.10.0 + latest_release: v0.11.0 stargazers_count: 4 - subscribers_count: 1 + subscribers_count: 2 topics: - singularity - manager @@ -84234,9 +84247,9 @@ cokelaer/pacbio4all: data_format: 2 description: pacbio tools filenames: - - singularity/Singularity.v1 - - singularity/Singularity.v2 - singularity/Singularity.v3 + - singularity/Singularity.v2 + - singularity/Singularity.v1 full_name: cokelaer/pacbio4all latest_release: null readme: '
This repository contains mini applications for\ + \ GPU Bootcamps. This bootcamp focuses on multi-GPU programming models.
\n\ +Scaling applications to multiple GPUs across multiple nodes requires one to\ + \ be adept at not just the programming models and optimization techniques, but\ + \ also at performing root-cause analysis using in-depth profiling to identify\ + \ and minimize bottlenecks. In this bootcamp, participants will learn to improve\ + \ the performance of an application step-by-step, taking cues from profilers along\ + \ the way. Moreover, understanding of the underlying technologies and communication\ + \ topology will help us utilize high-performance NVIDIA libraries to extract more\ + \ performance out of the system.
\nThis bootcamp requires\ + \ a multi-node system with multiple GPUs in each node (atleast 2 GPUs/ node).
\n\ +The total bootcamp\ + \ material would take approximately 8 hours .
\nA multi-node installation of NVIDIA's HPC SDK is desired. Refer to NVIDIA HPC SDK Installation Guide for detailed instructions.\ + \ Ensure that your installation contains HPCX with UCX.
\nAfter installation,\ + \ make sure to add HPC SDK to the environment as follows(For example the PATH\ + \ highlighted below is for HPC SDK 21.5):
\n
![\"PyPI](\"https://badge.fury.io/py/phigaro.svg\"\){kind=icon}
![\"Conda](\"https://anaconda.org/bioconda/phigaro/badges/installer/conda.svg\"\)
![\"Actions](\"https://github.com/bobeobibo/phigaro/workflows/Phigaro%20Tests/badge.svg\"\){kind=icon}
![\"Conda](\"https://anaconda.org/bioconda/phigaro/badges/version.svg\"\)
![\"License:](\"https://img.shields.io/badge/License-MIT-blue.svg\"\){kind=icon}
![\"macstadium\"](\"https://uploads-ssl.webflow.com/5ac3c046c82724970fc60918/5c019d917bba312af7553b49_MacStadium-developerlogo.png\"\)
![\"\](\"crispr-cas_logo.png\"){kind=logo}
![\"CRISPR-Cas++\"](\"crispr-cas_logo.png\"\){kind=logo}
![](\"http://www.pasteur-guadeloupe.fr/files/Workflow_CRISPRCasFinder.png\"\ "\\"CRISPRCasFinder")
![\"Current](\"https://img.shields.io/github/v/release/divonlan/genozip\"\ "\\"Current")
![\"Build](\"https://travis-ci.org/singularityware/singularity.svg?branch=master\"\)
![\"Forks\"](\"https://img.shields.io/github/forks/josephwkania/radio_transients?style=flat-square\"\)
![\"Stars\"](\"https://img.shields.io/github/stars/josephwkania/radio_transients?style=flat-square\"\)
![\"License\"](\"https://img.shields.io/github/license/josephwkania/radio_transients?style=flat-square\"\)
![\"Sylabs\"](\"https://img.shields.io/badge/Hosted-Sylabs-Green.svg\"\){kind=icon}
![\"https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg\"\](\"https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg\"\)
![\"Build\"](\"https://github.com/mazzalab/fastqwiper/actions/workflows/buildall_and_publish.yml/badge.svg\"\){kind=icon}
![\"codecov\"](\"https://codecov.io/gh/mazzalab/fastqwiper/graph/badge.svg?token=5V4AQTK619\"\){kind=icon}
![\"GitHub](\"https://img.shields.io/github/issues-raw/mazzalab/fastqwiper\"\)
![\"Anaconda-Server](\"https://anaconda.org/bfxcss/fastqwiper/badges/version.svg\"\)
![\"Anaconda-Server](\"https://anaconda.org/bfxcss/fastqwiper/badges/latest_release_date.svg\"\)
![\"Anaconda-Server](\"https://anaconda.org/bfxcss/fastqwiper/badges/platforms.svg\"\)
![\"Anaconda-Server](\"https://anaconda.org/bfxcss/fastqwiper/badges/downloads.svg\"\)
![\"PyPI](\"https://badge.fury.io/py/fastqwiper.svg\"\){kind=icon}
![\"PyPI](\"https://img.shields.io/pypi/pyversions/fastqwiper.svg\"\)
![\"PyPI](\"https://img.shields.io/pypi/dm/fastqwiper\"\)
![\"Docker](\"https://img.shields.io/docker/pulls/mazzalab/fastqwiper\"\)
![\"FastqWiper](\"assets/hierarchy.png\")
![](\"https://github.com/mazzalab/fastqwiper/blob/main/pipeline/fix_wipe_pairs_reads.png?raw=true\"\)
![](\"https://github.com/mazzalab/fastqwiper/blob/main/pipeline/fix_wipe_single_reads.png?raw=true\"\)
![\"Tweeting\"](\"https://img.shields.io/twitter/url/http/shields.io.svg?style=social\"\)
![\"Singularity\"](\"http://singularity.lbl.gov/images/logo/logo.svg\"){kind=logo}
![\"Docker\"](\"https://www.docker.com/sites/default/files/vertical.png\"\)
![\"Singularity](\"https://singularityhub.github.io/sregistry/assets/img/logo.png\"\){kind=logo}
# Add HPC-SDK to PATH:\n\
+ export PATH=\"<path-to-nvidia-hpc-sdk>/Linux_x86_64/21.5/compilers/bin:<path-to-nvidia-hpc-sdk>/Linux_x86_64/21.5/cuda/bin:$PATH \"\n# Add HPC-SDK to LD_LIBRARY_PATH:\n\
+ export LD_LIBRARY_PATH=\" <path-to-nvidia-hpc-sdk>/Linux_x86_64/21.5/comm_libs/nvshmem/lib:<path-to-nvidia-hpc-sdk>/Linux_x86_64/21.5/comm_libs/nccl/lib:<path-to-nvidia-hpc-sdk>/Linux_x86_64/21.5/comm_libs/mpi/lib:<path-to-nvidia-hpc-sdk>/Linux_x86_64/21.5/math_libs/lib64:<path-to-nvidia-hpc-sdk>/Linux_x86_64/21.5/compilers/lib:<path-to-nvidia-hpc-sdk>/Linux_x86_64/21.5/cuda/extras/CUPTI/lib64:<path-nvidia-hpc-sdk>>/Linux_x86_64/21.5/cuda/lib64:$LD_LIBRARY_PATH\"\n\
+ #ADD NVSHMEM HOME DIRECTORY PATH\n\
+ export CUDA_HOME=<path-to-nvidia-hpc-sdk>/Linux_x86_64/21.5/cuda\nexport\
+ \ NVSHMEM_HOME=<path-to-nvidia-hpc-sdk>/Linux_x86_64/21.5/comm_libs/nvshmem Note:\
+ \ If you don't use Slurm workload manager, remove --with-slurm flag.
Then, install OpenMPI as follows:
\n# Download and extract\
+ \ OpenMPI Tarfile\nwget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.1.tar.gz\n\
+ tar -xvzf openmpi-4.1.1.tar.gz\ncd openmpi-4.1.1/\n\
+ mkdir -p build\n# Configure OpenMPI\n\
+ ./configure --prefix=$PWD/build --with-libevent=internal\
+ \ --with-xpmem --with-cuda=<path-to-nvidia-hpc-sdk>/Linux_x86_64/21.5/cuda/ --with-slurm --enable-mpi1-compatibility\
+ \ --with-verbs --with-hcoll=<path-to-nvidia-hpc-sdk>/Linux_x86_64/21.5/comm_libs/hpcx/hpcx-2.8.1/hcoll/lib\
+ \ --with-ucx=<path-to-nvidia-hpc-sdk>/Linux_x86_64/21.5/comm_libs/hpcx/hpcx-2.8.1/ucx/\n# Install OpenMPI\nmake all install Now, add OpenMPI to the environment:
\nexport PATH=\"<path-to-openmpi>/build/bin/:$PATH\" \nexport LD_LIBRARY_PATH=\"<path-to-openmpi/build/lib:$LD_LIBRARY_PATH\" Ensure that the custom-built OpenMPI is in use by running which mpirun\
+ \ which should point the mpirun binary in <path-to-openmpi>/build/bin\
+ \ directory.
Multi-node compatible versions of the following\ + \ are required:
\nWe have tested all the codes with CUDA drivers 460.32.03 with CUDA 11.3.0.0,\ + \ OpenMPI 4.1.1, HPCX 2.8.1, Singularity 3.6.1, NCCL 2.9.9.1, and NVSHMEM 2.1.2.\ + \ Note that OpenMPI in our cluster was compiled with CUDA, HCOLL, and UCX support.
\n\ +As this\ + \ bootcamp covers multi-node CUDA-aware MPI concepts, it is primarily designed\ + \ to run without any containers. After the prerequisite softwares have been installed,\ + \ follow these steps to install and run Jupyter Lab:
\n#\
+ \ Install Anaconda3\nwget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh\
+ \ \nbash Miniconda3-latest-Linux-x86_64.sh -b -p <my_dir>\n#\
+ \ Add conda to PATH\nexport PATH=$PATH:<my_dir>/bin/\n# Install\
+ \ Jupyter Lab\nconda install -c conda-forge jupyterlab\n# Run Jupyter Lab\njupyter lab --notebook-dir=<path-to-gpubootcamp-repo>/hpc/multi_gpu_nways/labs/\
+ \ --port=8000 --ip=0.0.0.0 --no-browser --NotebookApp.token=\"\" After running Jupyter Lab, open http://localhost:8888 in a web browser and start the introduction.ipynb\
+ \ notebook.
This material is designed to primarily\ + \ run in containerless environments, that is, directly on the cluster. Thus, building\ + \ the Singularity container is OPTIONAL.
\nIf containerization is desired,\ + \ follow the steps outlined in the notebook MPI in Containerized Environments.
\nFollow the steps below to build\ + \ the Singularity container image and run Jupyter Lab:
\n#\
+ \ Build the container\nsingularity build multi_gpu_nways.simg Singularity\n\
+ # Run Jupyter Lab\nsingularity\
+ \ run --nv multi_gpu_nways.simg jupyter lab --notebook-dir=<path-to-gpubootcamp-repo>/hpc/multi_gpu_nways/labs/\
+ \ --port=8000 --ip=0.0.0.0 --no-browser --NotebookApp.token=\"\" Then, access Jupyter Lab on http://localhost:8888.
\nIf compiling any program\
+ \ throws an error related to CUDA/ NCCL/ NVHSMEM/ MPI libraries or header files\
+ \ being not found, ensure that LD_LIBRARY_PATH is correctly set.\
+ \ Moreover, make sure environment variables CUDA_HOME, NCCL_HOME,\
+ \ and NVSHMEM_HOME are set either during installation or manually\
+ \ inside each Makefile.
Please join\ + \ OpenACC Slack Channel to raise questions.
\nIf you observe any errors\ + \ or issues, please file an issue on GPUBootcamp GitHuB repository.
\n" + stargazers_count: 2 + subscribers_count: 1 + topics: + - cuda + - hpc + - mpi + - nccl + - nsight-systems + - nvshmem + updated_at: 1703680986.0 openhpc/ohpc: data_format: 2 description: OpenHPC Integration, Packaging, and Test Repo @@ -150194,8 +150836,8 @@ openhpc/ohpc: rel="nofollow">System Registration Form. ' - stargazers_count: 791 - subscribers_count: 87 + stargazers_count: 798 + subscribers_count: 86 topics: - hpc - scientific-computing @@ -150204,7 +150846,7 @@ openhpc/ohpc: - devtools - mpi - linuxfoundation - updated_at: 1702850438.0 + updated_at: 1705709363.0 opensciencegrid/osgvo-blaylockbk: data_format: 2 description: OSGVO image for blaylockbk @@ -150232,15 +150874,15 @@ oxfordmmm/preprocessing: data_format: 2 description: Mycobacterial pre-processing pipeline filenames: - - singularity/Singularity.ppFastqc - - singularity/Singularity.ppBedtools - - singularity/Singularity.ppPerljson - - singularity/Singularity.ppMykrobe - - singularity/Singularity.ppBowtie2 - - singularity/Singularity.ppFastp - - singularity/Singularity.ppKraken2 - singularity/Singularity.ppFqtools + - singularity/Singularity.ppBowtie2 + - singularity/Singularity.ppMykrobe + - singularity/Singularity.ppPerljson + - singularity/Singularity.ppBedtools - singularity/Singularity.ppBwa + - singularity/Singularity.ppFastqc + - singularity/Singularity.ppKraken2 + - singularity/Singularity.ppFastp full_name: oxfordmmm/preprocessing latest_release: null readme: '![\"GitHub](\"https://img.shields.io/github/license/phelelani/nf-rnaSeqCount\"\)
![\"fair-software.eu\"](\"https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8B-yellow\"\){kind=icon}
![\"GitHub](\"https://img.shields.io/github/stars/phelelani/nf-rnaSeqCount\"\)
nf-rnaSeqCount\
@@ -156434,14 +157076,208 @@ porchard/snRNAseq-NextFlow:
subscribers_count: 1
topics: []
updated_at: 1640263903.0
+pouya-codes/singularity_create_groups:
+ data_format: 2
+ description: null
+ filenames:
+ - Singularityfile.def
+ full_name: pouya-codes/singularity_create_groups
+ latest_release: null
+ readme: "
Before running any experiment to be sure you are\ + \ using the latest commits of all modules run the following script:
\n\ +![\"GitHub](\"https://img.shields.io/github/issues/phelelani/nf-rnaSeqCount\"\)
(cd /projects/ovcare/classification/singularity_modules ; ./update_modules.sh\
+ \ --bcgsc-pass your/bcgsc/path)\nusage: app.py [-h] {from-experiment-manifest,from-arguments} ...\n\n\
+ Splits patches to groups by patient case and saves the path to these patches in\
+ \ a group file (i.e. /path/to/patient_groups.json).\nThe patient_groups.json file\
+ \ uses Mitch's format for groups i.e. it is a json file with the format\n\n{\n\
+ \ \"chunks\": [\n {\n \"id\": int,\n \"imgs\"\
+ : list of paths to patches\n },\n ...DEAFULT_SEEDE || Total ||\n\
+ | Patient in Group 1 | 9 | 13 | 20 | 3 | 45 |\n| Patient in Group 2 | 9 | 13\
+ \ | 20 | 3 | 45 |\n| Patient in Group 3 | 8 | 13 | 20 | 3 | 44 |\n| Whole Slide\
+ \ Image | 38 | 63 | 79 | 13 | 193 |\n\n|| Patch Counts || MMRD || P53ABN || P53WT\
+ \ || POLE || Total ||\n| Patch in Group 1 | 38659 | 43918 | 52645 | 1791 | 137013\
+ \ |\n| Patch in Group 2 | 15261 | 71059 | 34979 | 17248 | 138547 |\n| Patch\
+ \ in Group 3 | 19431 | 51330 | 53700 | 7881 | 132342 |\n| Total | 73351 | 166307\
+ \ | 141324 | 26920 | 407902 |\n\nWhat are **categories**?\n\n1) if the --is_binary\
+ \ flag is used, then categories=('Tumor', 'Normal') where 'Tumor' is any patch\
+ \ annotated as 'Tumor' and 'Normal' is any patch with annotated as 'Other', 'MucinousBorderlineTumor',\
+ \ 'Necrosis' or 'Stroma'\n2) if the --is_binary flag is not used, then categories=subtype\
+ \ (i.e. CC, EC, MC, LGSC, HGSC)\n\n**balance_patches**:\n\nThe --balance_patches\
+ \ flag gives the following options (illustrated):\n\n1) `--balance_patches overall`\
+ \ sets every cell to the min cell.\nDEAFULT_SEEDll to the min cell in each group.\n\
+ \n|| Patch Counts || MMRD || P53ABN || P53WT || POLE || Total ||\n| Patch in\
+ \ Group 1 | 1791 | 1791 | 1791 | 1791 | 7164 |\n| Patch in Group 2 | 15261 |\
+ \ 15261 | 15261 | 15261 | 61044 |\n| Patch in Group 3 | 7881 | 7881 | 7881 |\
+ \ 7881 | 31524 |\n| Total | 24933 | 24933 | 24933 | 24933 | 99732 |\nset_random_seedup\
+ \ 1 | 30000 | 30000 | 30000 | 1791 | 91791 |\n| Patch in Group 2 | 15261 | 30000\
+ \ | 30000 | 17248 | 92509 |\n| Patch in Group 3 | 19431 | 30000 | 30000 | 7881\
+ \ | 87312 |\n| Total | 64692 | 90000 | 90000 | 26920 | 271612 |\n\n3) `--balance_patches\
+ \ group=cap_amt` caps the number of patches in every group by cap_amt.\n`--balance_patches\
+ \ group=135000`\n\n|| Patch Counts || MMRD || P53ABN || P53WT || POLE || Total\
+ \ ||\n| Patch in Group 1 | 38659 | 43918 | 50632 | 1791 | 135000 |\n| Patch\
+ \ in Group 2 | 15261 | 67512 | 34979 | 17248 | 135000 |\n| Patch in Group 3 |\
+ \ 19431 | 51330 | 53700 | 7881 | 132342 |\n| Total | 73351 | 162760 | 139311 |\
+ \ 26920 | 402342 |\n\n3) `--balance_patches category=cap_amt` caps the number\
+ \ of patches in every category by cap_amt.\n`--balance_patches category=100000`\n\
+ \n|| Patch Counts || MMRD || P53ABN || P53WT || POLE || Total ||\n| Patch in\
+ \ Group 1 | 38659 | 33333 | 33333 | 1791 | 107116 |\n| Patch in Group 2 | 15261\
+ \ | 33333 | 33333 | 17248 | 99175 |\n| Patch in Group 3 | 19431 | 33333 | 33333\
+ \ | 7881 | 93978 |\n| Total | 73351 | 99999 | 99999 | 26920 | 300269 |\n\n**max_patient_patches**:\n\
+ \nIf --max_patient_patches is set, then we will select max_patient_patches from\
+ \ each patient case, so if max_patient_patches=60 then we will select at most\
+ \ 60 patches across all slides belonging to the patient.\n\n (1) this will select\
+ \ patches uniformly across all slides belonging to the patient. For example if\
+ \ there are 3 slides, then we will sample 20 patches from each slide unless a\
+ \ few slides have <20 patches in which case we select >20 patches from the\
+ \ slides with enough patches until we have 60 in total.\n (2) this will select\
+ \ patches uniformly across all categories belonging to the patient. For example\
+ \ if categories=('Tumor', 'Normal') then we will select 30 patches each category\
+ \ unless one category has <30 slides in which case we select we select >30\
+ \ patches in the other category until we have 60 in total.\n (3) --max_patient_patches\
+ \ is applied before --balance_patches if both flags are set\n\npositional arguments:\n\
+ \ {from-experiment-manifest,from-arguments}\n Choose whether\
+ \ to use arguments from experiment manifest or from commandline\n from-experiment-manifest\n\
+ \ Use experiment manifest\n\n from-arguments Use\
+ \ arguments\n\noptional arguments:\n -h, --help show this help message\
+ \ and exit\n\nusage: app.py from-experiment-manifest [-h] [--component_id COMPONENT_ID]\n\
+ \ experiment_manifest_location\n\npositional\
+ \ arguments:\n experiment_manifest_location\n\noptional arguments:\n -h, --help\
+ \ show this help message and exit\n\n --component_id COMPONENT_ID\n\
+ \nusage: app.py from-arguments [-h] [--seed SEED] [--n_groups N_GROUPS]\n \
+ \ [--subtypes SUBTYPES [SUBTYPES ...]]\n \
+ \ [--is_binary] [--is_multiscale]\n \
+ \ [--balance_patches BALANCE_PATCHES]\n [--patch_pattern\
+ \ PATCH_PATTERN]\n [--filter_labels FILTER_LABELS\
+ \ [FILTER_LABELS ...]]\n --out_location OUT_LOCATION\n\
+ \ [--min_patches MIN_PATCHES]\n \
+ \ [--max_patches MAX_PATCHES]\n [--max_patient_patches\
+ \ MAX_PATIENT_PATCHES]\n {use-extracted-patches,use-hd5}\
+ \ ...\n\npositional arguments:\n {use-extracted-patches,use-hd5}\n \
+ \ Specify how to load patches.\n There\
+ \ are 2 ways of loading patches: by use_extracted_patches and by use_hd5.\n \
+ \ use-extracted-patches\n Use extracted and saved patches\n\
+ \n use-hd5 Use hd5 files\n\noptional arguments:\n -h, --help \
+ \ show this help message and exit\n\n --seed SEED Seed for\
+ \ random shuffle.\n (default: 256)\n\n --n_groups N_GROUPS\
+ \ The number of groups in groups file.\n (default: 3)\n\
+ \n --subtypes SUBTYPES [SUBTYPES ...]\n Space separated\
+ \ words describing subtype=groupping pairs for this study. Example: if doing one-vs-rest\
+ \ on the subtypes MMRD vs P53ABN, P53WT and POLE then the input should be 'MMRD=0\
+ \ P53ABN=1 P53WT=1 POLE=1'\n (default: {'MMRD': 0, 'P53ABN':\
+ \ 1, 'P53WT': 2, 'POLE': 3})\n\n --is_binary Whether we want to categorize\
+ \ patches by the Tumor/Normal category (true) or by the subtype category (false).\n\
+ \ (default: False)\n\n --is_multiscale Whether\
+ \ patches have multiple scales i.e. different magnifications. Not currently used.\n\
+ \ (default: False)\n\n --balance_patches BALANCE_PATCHES\n\
+ \ Optional method to balance patches. Can choose (1) ('group',\
+ \ 'overall', 'category') or (2) one of ('group=cap_amt', 'overall=cap_amt', 'category=cap_amt').In\
+ \ the case (1), we will balance out the patches in every group, category, or overall\
+ \ (see description for more details). In case (2), we will cap the number of patches\
+ \ in every group, category, or overall to the number cap_amt.\n \
+ \ (default: None)\n\n --patch_pattern PATCH_PATTERN\n \
+ \ '/' separated words describing the directory structure of the patch\
+ \ paths. The words are ('annotation', 'subtype', 'slide', 'patch_size', 'magnification').\
+ \ A non-multiscale patch can be contained in a directory /path/to/patch/rootdir/Tumor/MMRD/VOA-1234/1_2.png\
+ \ so its patch_pattern is annotation/subtype/slide. A multiscale patch can be\
+ \ contained in a directory /path/to/patch/rootdir/Stroma/P53ABN/VOA-1234/10/3_400.png\
+ \ so its patch_pattern is annotation/subtype/slide/magnification\n \
+ \ (default: annotation/subtype/slide)\n\n --filter_labels FILTER_LABELS\
+ \ [FILTER_LABELS ...]\n Space separated words describing\
+ \ label=value pairs to filter patch by label value. For example, if a dataset\
+ \ contains patche paths like path/to/patch/rootdir/Tumor/MMRD/VOA-1234/256/20/1_2.png\
+ \ and we want to select Tumor patches of pixel size 256 * 256 and 20x magnification\
+ \ then the patch_pattern is annotation/subtype/slide/patch_size/magnification\
+ \ and the select_labels is 'annotation=Tumor patch_size=256 magnification=20'\n\
+ \ (default: {})\n\n --out_location OUT_LOCATION\n \
+ \ full path of the groups file (i.e. /path/to/patient_groups.json).\
+ \ An example is '/projects/ovcare/classification/cchen/ml/data/local_ec_100/patient_groups.json'\n\
+ \ (default: None)\n\n --min_patches MIN_PATCHES\n \
+ \ Only include from slides that have at least min_patches\
+ \ number of patches\n (default: None)\n\n --max_patches\
+ \ MAX_PATCHES\n Only include from slides that have at most\
+ \ max_patches number of patches\n (default: None)\n\n\
+ \ --max_patient_patches MAX_PATIENT_PATCHES\n Select at\
+ \ most max_patient_patches number of patches from each patient.\n \
+ \ (default: None)\n\nusage: app.py from-arguments use-extracted-patches\
+ \ [-h] --patch_location\n PATCH_LOCATION\n\
+ \ {use-manifest,use-origin}\n\
+ \ ...\n\npositional arguments:\n\
+ \ {use-manifest,use-origin}\n Specify how to define patient\
+ \ ID and slide ID:\n 1. use-manifest 2. origin\n\
+ \ use-manifest Use manifest file to locate slides.\n \
+ \ a CSV file with minimum of 4 column and maximum of 6 columns.\
+ \ The name of columns\n should be among ['origin',\
+ \ 'patient_id', 'slide_id', 'slide_path', 'annotation_path', 'subtype'].\n \
+ \ origin, slide_id, patient_id must be one of the\
+ \ columns.\n\n use-origin Use origin for detecting patient ID and\
+ \ slide ID.\n NOTE: It only works for German, OVCARE,\
+ \ and TCGA.\n\noptional arguments:\n -h, --help show this help message\
+ \ and exit\n\n --patch_location PATCH_LOCATION\n root\
+ \ directory of all patches of a study. The patch directory structure is '/patch_location/patch_pattern/x_y.png'.\
+ \ See --patch_pattern below. An example is '/projects/ovcare/classification/cchen/ml/data/local_ec_100/patches_256_sorted'\n\
+ \ (default: None)\n\nusage: app.py from-arguments use-extracted-patches\
+ \ use-manifest\n [-h] --manifest_location MANIFEST_LOCATION\n\noptional\
+ \ arguments:\n -h, --help show this help message and exit\n\n --manifest_location\
+ \ MANIFEST_LOCATION\n Path to manifest CSV file.\n \
+ \ (default: None)\n\nusage: app.py from-arguments use-extracted-patches\
+ \ use-origin\n [-h] [--dataset_origin DATASET_ORIGIN [DATASET_ORIGIN ...]]\n\
+ \noptional arguments:\n -h, --help show this help message and exit\n\
+ \n --dataset_origin DATASET_ORIGIN [DATASET_ORIGIN ...]\n \
+ \ List of the origins of the slide dataset the patches are generated from.\
+ \ Should be from ('ovcare', 'tcga', 'german', 'other'). (For multiple origins,\
+ \ works for TCGA+ovcare. Mix of Other origins must be tested.)\n \
+ \ (default: ['ovcare'])\n\nusage: app.py from-arguments use-hd5 [-h]\
+ \ --hd5_location HD5_LOCATION\n {use-manifest,use-origin}\
+ \ ...\n\npositional arguments:\n {use-manifest,use-origin}\n \
+ \ Specify how to define patient ID and slide ID:\n \
+ \ 1. use-manifest 2. origin\n use-manifest Use manifest file\
+ \ to locate slides.\n a CSV file with minimum of\
+ \ 4 column and maximum of 6 columns. The name of columns\n \
+ \ should be among ['origin', 'patient_id', 'slide_id', 'slide_path',\
+ \ 'annotation_path', 'subtype'].\n origin, slide_id,\
+ \ patient_id must be one of the columns.\n\n use-origin Use origin\
+ \ for detecting patient ID and slide ID.\n NOTE:\
+ \ It only works for German, OVCARE, and TCGA.\n\noptional arguments:\n -h, --help\
+ \ show this help message and exit\n\n --hd5_location HD5_LOCATION\n\
+ \ root directory of all hd5 of a study.\n \
+ \ (default: None)\n\nusage: app.py from-arguments use-hd5 use-manifest\
+ \ [-h] --manifest_location\n \
+ \ MANIFEST_LOCATION\n\noptional arguments:\n -h, --help show this\
+ \ help message and exit\n\n --manifest_location MANIFEST_LOCATION\n \
+ \ Path to manifest CSV file.\n (default:\
+ \ None)\n\nusage: app.py from-arguments use-hd5 use-origin [-h]\n \
+ \ [--dataset_origin DATASET_ORIGIN [DATASET_ORIGIN\
+ \ ...]]\n\noptional arguments:\n -h, --help show this help message\
+ \ and exit\n\n --dataset_origin DATASET_ORIGIN [DATASET_ORIGIN ...]\n \
+ \ List of the origins of the slide dataset the patches are generated\
+ \ from. Should be from ('ovcare', 'tcga', 'german', 'other'). (For multiple origins,\
+ \ works for TCGA+ovcare. Mix of Other origins must be tested.)\n \
+ \ (default: ['ovcare'])\n\nTODO: there is a chance\ + \ --balance_patches sets empty groups. This happens if any patches for some (group,\ + \ category) is zero.\nTODO: in create_groups, variables are named 'subtype' instead\ + \ of 'category'. That leads to confusion.\nTODO: further explain how --max_patient_patches\ + \ works in description.\nTODO: make GroupCreator.group_summary() return DataFrame.\ + \ Test against DataFrame output.
\n" + stargazers_count: 0 + subscribers_count: 1 + topics: [] + updated_at: 1698864845.0 powellgenomicslab/Imputation_pipeline: data_format: 2 description: Imputation workflow with sanger impuation server, originally prepared for sceQTL-Gen consortium but copied here on 30 August, 2021 when updating to hg38 for sceQTL-Gen consortium filenames: - - Singularity.WGpipeline - Singularity.Imputation + - Singularity.WGpipeline full_name: powellgenomicslab/Imputation_pipeline latest_release: null readme: '![\"Status\"](\"https://github.com/pscedu/singularity-bamtools/actions/workflows/main.yml/badge.svg\"\){kind=icon}
\n![\"Issue\"](\"https://img.shields.io/github/issues/pscedu/singularity-bamtools\"\)
\n![\"forks\"](\"https://img.shields.io/github/forks/pscedu/singularity-bamtools\"\)
\n![\"Stars\"](\"https://img.shields.io/github/stars/pscedu/singularity-bamtools\"\)
\n![\"License\"](\"https://img.shields.io/github/license/pscedu/singularity-bamtools\"\)
\nSingularity\ - \ recipe for bamtools.
\n\ -Copy the
\nSIF filebamtools\
- \ scriptto /opt/packages/bamtools/2.5.1.
Copy\
- \ the file modulefile.lua to /opt/modulefiles/bamtools\
- \ as 2.5.1.
Run\
- \ the script build.sh to build image locally.
bash\
- \ ./build.sh\nRun the script rbuild.sh to build image locally.
bash\
- \ ./build.sh\nTo run the available tests, run the\ - \ command
\nbash ./test.sh\nCopyright \xA9\ - \ 2020-2021 Pittsburgh Supercomputing Center. All Rights Reserved.
\nThe\ - \ Biomedical\ - \ Applications Group at the Pittsburgh Supercomputing Center in the
\nSingularity recipe for bamtools.
\nCopy the
\nSIF\
+ \ filebamtools scriptto /opt/packages/bamtools/2.5.1.
Copy the file modulefile.lua to /opt/modulefiles/bamtools\
+ \ as 2.5.1.
Run the script build.sh to build image\
+ \ locally.
bash ./build.sh\nRun the script rbuild.sh to build image\
+ \ locally.
bash ./build.sh\nTo run the available tests, run the command
\nbash ./test.sh\n\
+ Copyright \xA9 2020-2021 Pittsburgh Supercomputing Center.\ + \ All Rights Reserved.
\nThe Biomedical Applications Group at the Pittsburgh Supercomputing Center in the Mellon College of Science at Carnegie Mellon University.
\n" stargazers_count: 0 @@ -160243,43 +161079,44 @@ pscedu/singularity-bcftools: noopener noreferrer\" href=\"https://github.com/pscedu/singularity-bcftools/actions/workflows/pretty.yml/badge.svg\"\ >![\"Status\"](\"https://github.com/pscedu/singularity-bcftools/actions/workflows/pretty.yml/badge.svg\"\){kind=icon}
\n![\"Issue\"](\"https://img.shields.io/github/issues/pscedu/singularity-bcftools\"\)
\n![\"forks\"](\"https://img.shields.io/github/forks/pscedu/singularity-bcftools\"\)
\n![\"Stars\"](\"https://img.shields.io/github/stars/pscedu/singularity-bcftools\"\)
\n![\"License\"](\"https://img.shields.io/github/license/pscedu/singularity-bcftools\"\)
\nSingularity\ - \ recipe for bcftools.
\n\ -Run the script build.sh to build image locally.
bash ./build.sh\nRun the script rbuild.sh to build image remotely.
bash\
- \ ./rbuild.sh\nTo run the available tests, run the\ - \ command
\nbash ./test.sh\nCopyright \xA9\ - \ 2020-2021 Pittsburgh Supercomputing Center. All Rights Reserved.
\nThe\ - \ Biomedical\ - \ Applications Group at the Pittsburgh Supercomputing\nCenter in the
\nSingularity recipe for bcftools.
\n\ +Run the script build.sh to build image\
+ \ locally.
bash ./build.sh\nRun the script rbuild.sh to build image\
+ \ remotely.
bash ./rbuild.sh\nTo run the available tests, run the command
\nbash ./test.sh\n\
+ Copyright \xA9 2020-2021 Pittsburgh Supercomputing Center.\ + \ All Rights Reserved.
\nThe Biomedical Applications Group at the Pittsburgh Supercomputing\nCenter in the Mellon College of Science at Carnegie Mellon University.
\n" stargazers_count: 0 @@ -160938,20 +161775,20 @@ pscedu/singularity-bsmap: noopener noreferrer\" href=\"https://github.com/pscedu/singularity-bsmap/actions/workflows/pretty.yml/badge.svg\"\ >![\"Status\"](\"https://github.com/pscedu/singularity-bsmap/actions/workflows/pretty.yml/badge.svg\"\){kind=icon}
\n![\"Issue\"](\"https://img.shields.io/github/issues/pscedu/singularity-bsmap\"\)
\n![\"forks\"](\"https://img.shields.io/github/forks/pscedu/singularity-bsmap\"\)
\n![\"Stars\"](\"https://img.shields.io/github/stars/pscedu/singularity-bsmap\"\)
\n![\"License\"](\"https://img.shields.io/github/license/pscedu/singularity-bsmap\"\)
\n![\"Status\"](\"https://github.com/pscedu/singularity-ncview/actions/workflows/pretty.yml/badge.svg\"\){kind=icon}
\n![\"Issue\"](\"https://img.shields.io/github/issues/pscedu/singularity-ncview\"\)
\n![\"forks\"](\"https://img.shields.io/github/forks/pscedu/singularity-ncview\"\)
\n![\"Stars\"](\"https://img.shields.io/github/stars/pscedu/singularity-ncview\"\)
\n![\"License\"](\"https://img.shields.io/github/license/pscedu/singularity-ncview\"\)
\nSingularity recipe for ncview.
\n![\"Status\"](\"https://github.com/pscedu/singularity-star-fusion/actions/workflows/main.yml/badge.svg\"\){kind=icon}
\n![\"Issue\"](\"https://img.shields.io/github/issues/pscedu/singularity-star-fusion\"\)
\n![\"forks\"](\"https://img.shields.io/github/forks/pscedu/singularity-star-fusion\"\)
\n![\"Stars\"](\"https://img.shields.io/github/stars/pscedu/singularity-star-fusion\"\)
\n![\"License\"](\"https://img.shields.io/github/license/pscedu/singularity-star-fusion\"\)
\nSingularity recipe for STAR-Fusion
\nCopy the
\n![](\"http://cirrus.ucsd.edu/~pierce/software/ncview/control_2.gif\"\)
SIF\
\ fileto /opt/packages/STAR-Fusion/1.11.1.
Copy the file modulefile.lua to /opt/modulefiles/STAR-Fusion\
\ as 1.11.1.lua.
Run the script build.sh to build image locally.
bash ./build.sh\nRun the script build.sh to build image\
+ \ locally.
bash ./build.sh\nRun the script rbuild.sh to build image\
\ remotely.
bash ./rbuild.sh\nTo run\ - \ the available tests, run the command
\nbash ./test.sh\nCopyright \xA9 2020-2022 Pittsburgh Supercomputing Center. All Rights\ - \ Reserved.
\nTo run the available tests, run the command
\nbash ./test.sh\n\
+ Copyright \xA9 2020-2022 Pittsburgh Supercomputing Center.\ + \ All Rights Reserved.
\nThe Biomedical Applications Group at the Pittsburgh Supercomputing Center in the Mellon College of Science at qbic-singularity-malt\n
A Singularity container with MALT, the\ @@ -174150,13 +174987,13 @@ sarahinwood/singularity-containers: data_format: 2 description: null filenames: - - Singularity.viralFlye_0.2.def - - Singularity.masurca_4.0.9.def - Singularity.plink_2.0.def - - Singularity.circos-0.69-9.def - - Singularity.bioconductor_3.14.def - Singularity.bioconductor_3.12.def + - Singularity.bioconductor_3.14.def - Singularity.BBMap_39.01.def + - Singularity.masurca_4.0.9.def + - Singularity.viralFlye_0.2.def + - Singularity.circos-0.69-9.def - Singularity.gemma_0.98.5.def full_name: sarahinwood/singularity-containers latest_release: null @@ -176978,7 +177815,7 @@ sequana/sequana: - singularity/Singularity.0_8_0 full_name: sequana/sequana latest_release: v0.16.5 - stargazers_count: 136 + stargazers_count: 137 subscribers_count: 7 topics: - ngs @@ -176990,7 +177827,7 @@ sequana/sequana: - snakemake - coverage - rna-seq - updated_at: 1703912799.0 + updated_at: 1705658745.0 sequana/variant_calling: data_format: 2 description: null @@ -179085,8 +179922,8 @@ singularityhub/circle-ci-sregistry: description: An example repository to deploy multiple containers to a Singularity Registry Server from CircleCI filenames: - - vanessa/greeting/Singularity - vanessa/greeting/Singularity.tag + - vanessa/greeting/Singularity full_name: singularityhub/circle-ci-sregistry latest_release: null readme: '
Singularity recipe for installing NEMO prerequisites, and scripts for configuring and running AMM7 model
@@ -185920,13 +186758,13 @@ sylabs/singularity: found in the license file. ' - stargazers_count: 604 + stargazers_count: 608 subscribers_count: 13 topics: - containers - hpc - linux - updated_at: 1705101965.0 + updated_at: 1705677877.0 sylvainschmitt/singularity-octopus: data_format: 2 description: 'octopus Singularity container ' @@ -187424,11 +188262,11 @@ tdalford/bilby_relative_binning: data_format: 2 description: null filenames: - - containers/Singularity.0.3.5 - - containers/Singularity.0.4.1 - containers/Singularity.0.4.0 - containers/Singularity.0.3.3 + - containers/Singularity.0.3.5 - containers/Singularity.0.3.6 + - containers/Singularity.0.4.1 full_name: tdalford/bilby_relative_binning latest_release: null stargazers_count: 0 @@ -187439,26 +188277,26 @@ team113sanger/t113-singularity: data_format: 2 description: null filenames: + - recipes/Singularity.seqtk__1.3 + - recipes/Singularity.kallisto__0.46.0__hb6a4e58_0 + - recipes/Singularity.fqtools__2.2 - recipes/Singularity.fastqc__0.11.8__1 - - recipes/Singularity.nextflow__19.01.0__ha4d7672_4 + - recipes/Singularity.BAGEL__0.9 - recipes/Singularity.STAR-Fusion__1.6.0 - - recipes/Singularity.kallisto__0.46.0__hb6a4e58_0 - - recipes/Singularity.mageck__0.5.8__py36h3e44d54_0 - - recipes/Singularity.jq__1.6_0 + - recipes/Singularity.nextflow__19.01.0__ha4d7672_4 - recipes/Singularity.DEAGO__1.0.0 - - recipes/Singularity.BAGEL__0.9 - - recipes/Singularity.fqtools__2.2 - - recipes/Singularity.multiqc__1.7__py_2 - recipes/Singularity.fqtools__2.0__hf50d5a6_4 - - recipes/Singularity.seqtk__1.3 - - recipes/R/Singularity.R-3.6.0.subclonal_reconstruction-1.0.0 - - recipes/R/Singularity.R-3.6.0.base-1.0.0 + - recipes/Singularity.multiqc__1.7__py_2 + - recipes/Singularity.jq__1.6_0 + - recipes/Singularity.mageck__0.5.8__py36h3e44d54_0 - recipes/R/Singularity.R-3.6.0.methylation-1.0.0 - recipes/R/Singularity.R-3.6.0.base-1.0.1 + - recipes/R/Singularity.R-3.6.0.subclonal_reconstruction-1.0.0 + - recipes/R/Singularity.R-3.6.0.base-1.0.0 full_name: team113sanger/t113-singularity latest_release: null readme: '![\"GitHub](\"https://github.com/twesterhout/spin-ed/workflows/CI/badge.svg\"\){kind=icon}
\nSpinED\n
![\"\](\"https://github.com/twesterhout/spin-ed/workflows/CI/badge.svg\"){kind=icon}
\n![\"GitHub](\"https://img.shields.io/github/v/release/twesterhout/spin-ed?include_prereleases\"\)
\n
User-friendly exact diagonalization\ \ package for quantum many-body systems.
\nWe provide pre-built static executables\
- \ for Linux. Go to\nReleases page and download the\nexecutable to your location of choice. That's\
- \ it!
\n\n\n
\u2139\uFE0F Note: executables are currently tagged\ - \ by git\ncommits from which they were built. It is suggested that after downloading\n\ - the application you create a symbolic link to it:\n\ -ln --symbolic SpinED SpinED-8b0138b # the commit hash may differ in your case
Using SpinED is quite simple.\
- \ Just feed it your input yaml\nfile. For example:
We provide pre-built static executables for Linux. Go to\n\ + Releases page\ + \ and download the\nexecutable to your location of choice. That's it! \U0001F973\ +
\n
![\"BSD-3-Clause](\"https://img.shields.io/badge/license-BSD--3--Clause-blue.svg\"\){kind=icon}
\n\u2139\uFE0F Note: executables are currently\
+ \ tagged by git\ncommits from which they were built. It is suggested that after\
+ \ downloading\nthe application you create a symbolic link to it:
\nln --symbolic SpinED SpinED-8b0138b # the commit hash may differ in your\
+ \ case
\n\nUsing\
+ \ SpinED is quite simple. Just feed it your input yaml\nfile. For example:
./SpinED my_system.yamlwhere my_system.yaml\
\ looks like this:
basis:\n number_spins:\
@@ -191777,15 +192611,15 @@ twesterhout/spin-ed:
\ was a very simple example! Have a look at template.yaml\n\
which describes all supported fields. example/\
\ folder also\ncontains various usage examples.\n
\nIf you use this package for your research and have questions\
\ or suggestions,\nplease, don't hesitate to contact me on Github or\nemail.
\n\
Also, if the fact that most code here is written in Haskell doesn't scare you,\n\
feel free to create a pull request implementing new features or fixing bugs!
\n"
- stargazers_count: 15
- subscribers_count: 3
+ stargazers_count: 16
+ subscribers_count: 4
topics:
- exact-diagonalization
- quantum
@@ -191793,7 +192627,7 @@ twesterhout/spin-ed:
- high-performance
- haskell
- numerical-methods
- updated_at: 1684044129.0
+ updated_at: 1697897886.0
twongjirad/singularity-genie-deps-root5-ubuntu14.04:
data_format: 2
description: Singularity Image for GENIE dependencies built with ROOT5 on Ubuntu
@@ -192572,7 +193406,7 @@ uit-no/apptainer-mathematica:
'
stargazers_count: 0
- subscribers_count: 3
+ subscribers_count: 4
topics: []
updated_at: 1692957745.0
uncch-rdmc/singularity-dev-images:
@@ -195247,7 +196081,7 @@ virajmehta/bats:
'
stargazers_count: 2
- subscribers_count: 3
+ subscribers_count: 4
topics: []
updated_at: 1689237237.0
vissed-kad/github_demo:
@@ -196847,53 +197681,53 @@ vsoch/robotname:
pl-s\">`seq 1 10`;\n do\n docker run\
\ vanessa/robotname badge\ndone ![\"https://img.shields.io/badge/zippy-ricecake_8984-mediumslateblue.svg?style=flat&link=https%3A%2F%2Fopenbases.github.io%2Fopenbases-python%2Fhtml%2Fusage.html%23badges&longCache=true\"\](\"https://img.shields.io/badge/zippy-ricecake_8984-mediumslateblue.svg?style=flat&link=https%3A%2F%2Fopenbases.github.io%2Fopenbases-python%2Fhtml%2Fusage.html%23badges&longCache=true\"\){kind=icon}
![\"https://img.shields.io/badge/pusheena-bicycle_8254-palevioletred.svg?style=flat&link=https%3A%2F%2Fopenbases.github.io%2Fopenbases-python%2Fhtml%2Fusage.html%23badges&longCache=true\"\](\"https://img.shields.io/badge/pusheena-bicycle_8254-palevioletred.svg?style=flat&link=https%3A%2F%2Fopenbases.github.io%2Fopenbases-python%2Fhtml%2Fusage.html%23badges&longCache=true\"\){kind=icon}
![\"https://img.shields.io/badge/carniverous-train_5364-chocolate.svg?style=flat&link=https%3A%2F%2Fopenbases.github.io%2Fopenbases-python%2Fhtml%2Fusage.html%23badges&longCache=true\"\](\"https://img.shields.io/badge/carniverous-train_5364-chocolate.svg?style=flat&link=https%3A%2F%2Fopenbases.github.io%2Fopenbases-python%2Fhtml%2Fusage.html%23badges&longCache=true\"\){kind=icon}
![\"https://img.shields.io/badge/blank-chestnut_3279-slategray.svg?style=flat&link=https%3A%2F%2Fopenbases.github.io%2Fopenbases-python%2Fhtml%2Fusage.html%23badges&longCache=true\"\](\"https://img.shields.io/badge/blank-chestnut_3279-slategray.svg?style=flat&link=https%3A%2F%2Fopenbases.github.io%2Fopenbases-python%2Fhtml%2Fusage.html%23badges&longCache=true\"\){kind=icon}
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![\"https://img.shields.io/badge/fat-latke_1119-turquoise.svg?style=flat&link=https%3A%2F%2Fopenbases.github.io%2Fopenbases-python%2Fhtml%2Fusage.html%23badges&longCache=true\"\](\"https://img.shields.io/badge/fat-latke_1119-turquoise.svg?style=flat&link=https%3A%2F%2Fopenbases.github.io%2Fopenbases-python%2Fhtml%2Fusage.html%23badges&longCache=true\"\){kind=icon}
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![\"https://img.shields.io/badge/purple-earthworm_2677-rebeccapurple.svg?style=flat&link=https%3A%2F%2Fopenbases.github.io%2Fopenbases-python%2Fhtml%2Fusage.html%23badges&longCache=true\"\](\"https://img.shields.io/badge/purple-earthworm_2677-rebeccapurple.svg?style=flat&link=https%3A%2F%2Fopenbases.github.io%2Fopenbases-python%2Fhtml%2Fusage.html%23badges&longCache=true\"\){kind=icon}
Brought to you by sdaps_container + tabindex="-1" href="#sdaps_container">sdaps_container
Singularity Container for SDAPS
-The methods used in this module are described in docs/methods.pdf.\
- \ TODO: docs/methods.pdf
Below is the structure of the results\
- \ directory. The values that will be listed in description_of_params\
- \ within the directory structure correspond to the various parameters one can\
- \ set. An example of a paramters file is found in example_runtime_setup/params.yml.
![\"https://img.shields.io/badge/zippy-leg_0162-palegreen.svg?style=flat&link=https%3A%2F%2Fopenbases.github.io%2Fopenbases-python%2Fhtml%2Fusage.html%23badges&longCache=true\"\](\"https://img.shields.io/badge/zippy-leg_0162-palegreen.svg?style=flat&link=https%3A%2F%2Fopenbases.github.io%2Fopenbases-python%2Fhtml%2Fusage.html%23badges&longCache=true\"\){kind=icon}
nf-qc_cluster\n\u251C\u2500\
- \u2500 normalization_001::description_of_params\n\u2502 \u251C\u2500\u2500 [files:\
- \ data]\n\u2502 \u251C\u2500\u2500 reduced_dims-pca::description_of_params\n\
+ readme: "Description
\nThe methods used in this\
+ \ module are described in docs/methods.pdf. TODO: docs/methods.pdf
\n\
+ Below is the structure of the results directory. The values that will be listed\
+ \ in description_of_params within the directory structure correspond\
+ \ to the various parameters one can set. An example of a paramters file is found\
+ \ in example_runtime_setup/params.yml.
\nnf-qc_cluster\n\u251C\u2500\u2500 normalization_001::description_of_params\n\
+ \u2502 \u251C\u2500\u2500 [files: data]\n\u2502 \u251C\u2500\u2500 reduced_dims-pca::description_of_params\n\
\u2502 \u2502 \u251C\u2500\u2500 [files: data]\n\u2502 \u2502 \u251C\u2500\
\u2500 [plots: umap]\n\u2502 \u2502 \u251C\u2500\u2500 cluster_001::description_of_params\n\
\u2502 \u2502 \u2502 \u251C\u2500\u2500 [files: data,clusters]\n\u2502 \
@@ -199342,30 +200177,32 @@ wtsi-hgi/nf_cellbender:
\ ... etc. ...\n\u251C\u2500\u2500 normalization_002::description_of_norm_params\n\
... etc. ...\n\u2514\u2500\u2500 adata.h5 # concatenated single cell data with no normalization\n\
- TODO list
\n\
- docs/methods.pdf file.scanpy_merge-dev.py:\
- \ If it were important to have a per sample filter, merge could be re-designed\
- \ to accommodate this.scanpy_cluster.py: Currently for\
- \ clustering, we can change method (leiden or louvain), resolution, and n_pcs.\
- \ Are there other parameters that need to be scaled over?docs/methods.pdf file.scanpy_merge-dev.py: If it were important\
+ \ to have a per sample filter, merge could be re-designed to accommodate this.scanpy_cluster.py: Currently for clustering, we can change\
+ \ method (leiden or louvain), resolution, and n_pcs. Are there other parameters\
+ \ that need to be scaled over?Quickstart for deploying\ - \ this pipeline locally and on a high performance compute cluster.
\nInstall the required packages via conda:
\nQuickstart for deploying this pipeline locally and on a high performance compute\ + \ cluster.
\nInstall the required packages via conda:
\n