sschmeier/simg-txid:201902
$ singularity pull shub://sschmeier/simg-txid:201902
Singularity Recipe
Bootstrap: docker
From: continuumio/miniconda3:4.5.12
%labels
AUTHOR schmeier@tuta.io
%environment
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# This sets global environment variables for anything run within the container
export PATH="/opt/conda/bin:/usr/local/bin:/usr/bin:/bin:"
unset CONDA_DEFAULT_ENV
export ANACONDA_HOME=/opt/conda
%post
export PATH=/opt/conda/bin:$PATH
echo "We add conda channels."
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
echo "We install tools."
conda install --yes pybedtools pysam sambamba=0.6.8 salmon=0.12.0 star=2.7.0d samtools=1.9 gffread=0.9.9 bioawk=1.0 ucsc-gtftogenepred=377 circexplorer2=2.3.5 bedtools=2.27.1 pandas=0.23.3 colorama=0.3.9 rseqc=2.6.4 cpat=1.2.3 picard=2.18.26 r-readr=1.3.1 r-samr=2.0 bioconductor-tximport=1.10.0 bioconductor-deseq2=1.22.1 bioconductor-limma=3.38.3 bioconductor-edger=3.24.1 bioconductor-ihw=1.10.0 multiqc=1.7
conda clean --index-cache --tarballs --packages --yes
Collection
- Name: sschmeier/simg-txid
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/sschmeier-simg-txid-201902 |
collection name | sschmeier/simg-txid |
branch | master |
tag | 201902 |
commit | 36604631b8642239c621ac904501654ef2539c6a |
version (container hash) | fa5f7b2493d26280494935ae4b7cb6cf |
build date | 2019-02-24T08:38:40.274Z |
size (MB) | 3807 |
size (bytes) | 1326727199 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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