Skip to content

Instantly share code, notes, and snippets.

@IsmailM

IsmailM/codex installation

Created June 10, 2020 11:08
Show Gist options
  • Save IsmailM/70ed70591a47b5a29084c3e29a88b4ed to your computer and use it in GitHub Desktop.
Save IsmailM/70ed70591a47b5a29084c3e29a88b4ed to your computer and use it in GitHub Desktop.
Download ZIP

Revisions

  1. IsmailM created this gist Jun 10, 2020.
    17 changes: 17 additions & 0 deletions codex installation
    View file
    Original file line number Diff line number Diff line change
    @@ -0,0 +1,17 @@
    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"]