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odinokov/install_ichorCNA.sh

Created April 17, 2023 07:00
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How to install ichorCNA
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install_ichorCNA.sh
mamba create --name ichorCNA && \
mamba activate ichorCNA && \
mamba install -y -c conda-forge -c bioconda r-essentials r-base r-devtools hmmcopy bioconductor-genomeinfodb bioconductor-genomicranges r-ichorcna && \
cd $CONDA_PREFIX/lib/R/library/ichorCNA/ && \
mkdir -p tmp && \
git clone https://github.com/broadinstitute/ichorCNA.git tmp && \
cp -r ./tmp/scripts/ .
# dry-run
Rscript $CONDA_PREFIX/lib/R/library/ichorCNA/scripts/runIchorCNA.R
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