README.rst

Deprecated

These packages migrated to the bioconda <https://github.com/bioconda/bioconda-recipes>_ community project. bioconda is the best source for up to date biological packages for conda. If you have interest in any non-migrated tools, feel free to use these recipes or raise a pull request for us to move them to bioconda.

If you're using the bcbio channel with conda, update to bioconda with::

conda config --remove channels bcbio
conda config --add channels bioconda

bcbio-conda

conda <http://conda.pydata.org/docs/>_ recipes for bcbio-nextgen <https://github.com/chapmanb/bcbio-nextgen>_ and bcbio-nextgen-vm <https://github.com/chapmanb/bcbio-nextgen-vm>_.

To build and upload for a specific platform, first ask Brad <http://github.com/chapmanb>_ for permission to write to the bcbio organization. You will need to have conda and anaconda available on your PATH and conda-build installed::

conda install conda anaconda-client conda-build

Then run::

python update_binstar_packages.py

If you need to build libraries with C extensions on Linux, use a CentOS 5.x container::

docker run --net=host -i -t -v pwd:/tmp/bcbio-conda centos:centos5 /bin/bash /tmp/bcbio-conda/update_binstar_packages_docker.sh

The scripts will query available packages and try to build and upload any that are not present. Depending on your system you may not be able to build some packages. For instance, you can't create Mac OSX packages on Linux when they contain C extensions.

To use these packages, add the bcbio conda channel <https://anaconda.org/bcbio>_::

conda config --add channels bcbio

To maintain compatibility, we build packages with:

• numpy 1.10
• CentOS 5.x (using docker with centos:centos5)