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conda

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    Remove math-round dep
    Sébastien Moretti authored
    f8b23d76
    History
    user avatar f8b23d76
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    Name Last commit Last update
    ..
    README.md
    build.sh
    meta.yaml
    README.md

    Conda build HOWTO

    https://docs.conda.io/projects/conda-build/en/latest/user-guide/tutorials/build-pkgs.html

    Build locally chipseq in conda

    conda build meta.yaml -c bioconda

    Install locally chipseq in local conda

    conda install -c bioconda --use-local chipseq

    See https://stackoverflow.com/questions/56895109/how-to-fix-unsatisfiableerror-the-following-specifications-were-found-to-be-in if unsatisfiableerror

    Converting a package for use on all platforms

    conda convert --platform all ~/miniconda3/conda-bld/linux-64/chipseq-*.tar.bz2 -o outputdir/
#OR TO SKIP win BUILDS
for proc in {osx-64,osx-arm64,linux-32,linux-64,linux-ppc64,linux-ppc64le,linux-s390x,linux-armv6l,linux-armv7l,linux-aarch64};
    do conda convert --platform $proc ~/miniconda3/conda-bld/linux-64/chipseq-*.tar.bz2 -o outputdir/;
done
#TO DEAL WITH grep requirement only for x84_64 currently
#ALSO an issue with libgcc-ng (the GCC low-level runtime library) on Mac x86_64. Don't know how to replace it
for proc in {osx-64,linux-64};
    do conda convert --platform $proc ~/miniconda3/conda-bld/linux-64/chipseq-*.tar.bz2 -o outputdir/;
done

    Uploading new packages to Anaconda.org

    After converting your files for use on other platforms, you may choose to upload your files to Anaconda.org.

    1. If you have not done so already, open a free Anaconda.org account and record your new username and password
    2. Run the command conda install anaconda-client, and then enter your Anaconda.org username and password
    3. Log into your Anaconda.org account with the command:
    anaconda login
    1. Upload your package to Anaconda.org (with -u sibswiss to upload in the sibswiss organization)
    anaconda upload -u sibswiss ~/miniconda3/conda-bld/linux-64/chipseq-*.tar.bz2 outputdir/*/chipseq-*.tar.bz2
    1. Logout
    anaconda logout

    Install the chipseq package from anaconda

    conda create --name chipseq                       # Create an isolated environment
conda activate chipseq                            # Use this environment
conda install -c sibswiss -c bioconda chipseq     # Install chipseq using the sibswiss and secondaryly the bioconda organizations
chipcor -h                                        # Test chipseq tools
conda deactivate                                  # Go out of the chipseq environment