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IsmailM/codex installation

Created June 10, 2020 11:08
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codex installation
FROM biocontainers/biocontainers:latest
USER root
RUN conda install samtools=1.3.1 bioconductor-wes.1kg.wugsc r-optparse \
r-data.table r-devtools r-curl r-xml r-biocmanager
RUN ln -s /bin/tar /bin/gtar
# Other R dependencies
RUN Rscript -e "BiocManager::install('CODEX')"
# RUN Rscript -e "devtools::install_github('yuchaojiang/CODEX2/package')"
ADD . /analysis
WORKDIR /analysis
CMD ["bin", "bash"]
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