sschmeier/simg-lncrna:latest
$ singularity pull shub://sschmeier/simg-lncrna:latest
Singularity Recipe
Bootstrap: docker
From: continuumio/miniconda3:4.5.11
%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 kallisto=0.45.0 salmon=0.12.0 star=2.6.1b samtools=1.9 stringtie=1.3.4 gffcompare=0.10.1 gffread=0.9.9 bioawk=1.0 ucsc-gtftogenepred=366 circexplorer2=2.3.3 bedtools=2.27.1 pandas=0.23.3 colorama=0.3.9 rseqc=2.6.4 cpat=1.2.3 r-readr=1.1.1 r-samr=2.0 bioconductor-tximport=1.8.0 bioconductor-deseq2=1.20.0 bioconductor-limma=3.36.5 bioconductor-edger=3.22.5 bioconductor-ihw=1.8.0 multiqc=1.6a0
conda clean --index-cache --tarballs --packages --yes
Collection
- Name: sschmeier/simg-lncrna
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/sschmeier-simg-lncrna-latest |
collection name | sschmeier/simg-lncrna |
branch | master |
tag | latest |
commit | e6527574bc30edd8cb953a23131c29d8cc9a3b18 |
version (container hash) | dccfbe86a9a565c035bbc0c5eeed147a |
build date | 2018-12-20T11:05:47.372Z |
size (MB) | 3147 |
size (bytes) | 988446751 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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