Binaries

Prebuilt binaries

To ease installation of the many tools and libraries, we distribute binaries that should work for most Linux users. If you have a problem, file an issue and we might be able to help.

Obtaining prebuilt binaries

A tarball will be available on our "cloud" servers. Soon. (July 2017)

Which binary do I need?

That depends on your python2.7 Unicode size.

python2.7 -c 'import sysconfig,pprint; pprint.pprint(sysconfig.get_config_vars()["Py_UNICODE_SIZE"])'

(We do not support python3.)

Installing prebuilt binaries

After downloading a tarball, you will simply untar into a Python distribution. You have 3 choices:

1. Python virtualenv
2. Python userbase
3. Standard Python installation

Let's call the root directory of you python installation ${PREFIX} and the path to your tarball ${TARBALL}.

virtualenv

We assume you know how to install, create, and activate a virtualenv.

virtualenv ${PREFIX}
source ${PREFIX}/bin/activate
tar xvzf ${TARBALL} ${PREFIX}
export LD_LIBRARY_PATH=${PREFIX}/lib:${LD_LIBRARY_PATH}

userbase

export PYTHONUSERBASE=${PREFIX}
tar xvzf ${TARBALL} ${PREFIX}
export LD_LIBRARY_PATH=${PREFIX}/lib:${LD_LIBRARY_PATH}
export PATH=${PREFIX}/bin:${PATH}

Standard

Typically, /usr/local

sudo tar xvzf ${TARBALL} ${PREFIX}
export LD_LIBRARY_PATH=${PREFIX}/lib:${LD_LIBRARY_PATH}
export PATH=${PREFIX}/bin:${PATH}

Try it!

samtools --help
pbalign --help
variantCaller -h
python2.7 -c 'import pysam; print pysam'
python2.7 -c 'import h5py; print h5py'