sschmeier/simg-rnaseq:202005

$ singularity pull shub://sschmeier/simg-rnaseq:202005

Singularity Recipe

Bootstrap: docker
From: continuumio/miniconda3

%labels
   AUTHOR s.schmeier@pm.me

%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 salmon=1.1.0 star=2.7.3a bbmap=38.76 fastp=0.20.0 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 multiqc samtools rseqc gffutils sambamba seqtk fastqc htseq subread
   conda clean --index-cache --tarballs --packages --yes

Collection


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Metrics

key value
id /containers/sschmeier-simg-rnaseq-202005
collection name sschmeier/simg-rnaseq
branch master
tag 202005
commit 61589847eb89da8b6080a54dfa38620998e861e7
version (container hash) 4a824a68180a0dd08f310ebddd3cc296fbf9d340e5c061c783108cbf8695974b
build date 2020-08-18T06:42:22.068Z
size (MB) 1220.88671875
size (bytes) 1280192512
SIF Download URL (please use pull with shub://)
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