sschmeier/simg-rnaseq:201907
$ singularity pull shub://sschmeier/simg-rnaseq:201907
Singularity Recipe
Bootstrap: docker
From: continuumio/miniconda3
%labels
AUTHOR s.schmeier@protonmail.com
%environment
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# This sets global environment variables for anything run within the container
export PATH="/opt/conda/bin:$PATH"
unset CONDA_DEFAULT_ENV
export ANACONDA_HOME=/opt/conda
%post
export PATH=/opt/conda/bin:$PATH
#conda update --yes -q conda
echo "We add conda channels."
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
echo "We install tools."
conda install --yes r-samr bioconductor-deseq2 bioconductor-edger r-readr bioconductor-limma bioconductor-ihw bioconductor-tximport bioconductor-biocparallel bioconductor-clusterprofiler bioconductor-org.hs.eg.db bioconductor-org.mm.eg.db bioconductor-gseabase colorama pandas numpy star=2.7.1a multiqc=1.7 bbmap=38.51 samtools=1.9 rseqc=3.0.0 salmon=0.14.1 gffutils=0.9 sambamba=0.7.0 seqtk=1.3 fastp=0.20.0 fastqc=0.11.8 htseq
conda clean --index-cache --tarballs --packages --yes
Collection
- Name: sschmeier/simg-rnaseq
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/sschmeier-simg-rnaseq-201907 |
collection name | sschmeier/simg-rnaseq |
branch | master |
tag | 201907 |
commit | 1cbf4e73e46193968a1e697bdd884430dedd3d15 |
version (container hash) | 285705544107256549191175558aa555942a4ed713b117814b5da99abaf7873c |
build date | 2020-12-03T11:53:56.263Z |
size (MB) | 1180.0390625 |
size (bytes) | 1237360640 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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