sschmeier/simg-rnaseq:202002
$ singularity pull shub://sschmeier/simg-rnaseq:202002
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 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
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-202002 |
collection name | sschmeier/simg-rnaseq |
branch | master |
tag | 202002 |
commit | eacea90cc60a66282a9efc85079617b9114fa17f |
version (container hash) | 009c72805d33cbcd3961d14564ef1aac68cfa0d94d99921cf3c49ddfece34a81 |
build date | 2020-05-28T12:23:10.888Z |
size (MB) | 1375.71875 |
size (bytes) | 1442545664 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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