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"]