sschmeier/simg-rnaseq:201906

$ singularity pull shub://sschmeier/simg-rnaseq:201906

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=0.14.0 gffutils=0.9 sambamba=0.7.0 seqtk=1.3 fastp=0.20.0 fastqc=0.11.8
   conda clean --index-cache --tarballs --packages --yes

Collection


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Metrics

key value
id /containers/sschmeier-simg-rnaseq-201906
collection name sschmeier/simg-rnaseq
branch master
tag 201906
commit 26f741e6a5ffe39f87b9bc9d993cca865afcd0dc
version (container hash) c8f8c9e3ed65033b0549ca99e0f3d295
build date 2020-11-19T09:58:18.257Z
size (MB) 3831
size (bytes) 1313349663
SIF Download URL (please use pull with shub://)
Datalad URL View on Datalad
Singularity Recipe Singularity Recipe on Datalad
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