Parabam

Parabam is a tool for processing sequencing files in parallel. It uses pythons native multiprocessing framework to apply a user defined rule on an input file.

Full documentation can be found here.

INSTALL

Installation is via pip.

# current release
pip install parabam
# specific version
pip install parabam==$VERSION

Note: pip install parabam does not work for 2.3.1/3.0.0 use the following:

export VERSION=X.X.X
# directly from GitHub (incase pypi release hasn't been performed)
pip install https://github.com/cancerit/parabam/releases/download/$VERSION/parabam-${VERSION}.tar.gz

Package Dependancies

pip will install the relevant dependancies, listed here for convenience:

numpy
pysam

Development Dependencies

Setup VirtualEnv

Parabam is a Cython package. In order to set it up for development use, you'll need to install Cython to compile .pyx files to .c files.

Note: Whenever you need to test changes you've made in .pyx files, you'll need to do python setup.py sdist && python setup.py develop, otherwise, those changes are not effective.

cd $PROJECTROOT
hash virtualenv || pip3 install virtualenv
python3 -m venv env
source env/bin/activate
pip3 install cython  # in order to be able to compile pyx files
python setup.py sdist  # compile pyx files into c files
python setup.py develop  # install parabam or update existing installation

Create a release

As for 2.3.0 and later, this package is not published on PyPI, to ease its installation, we should upload it's cython compiled package with each of our release. You'll need to run python setup.py sdist to build the compiled package, and then upload the tar.gz file in dist folder as an attachment with each release.