Binaries - PacificBiosciences/FALCON_unzip GitHub Wiki

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

Tarballs are available on our "cloud" servers: https://downloads.pacbcloud.com/public/falcon/

Example:

curl -O https://downloads.pacbcloud.com/public/falcon/falcon-...gz

Which binary do I need?

That depends on your python2.7 Unicode size. Almost certainly, you want "ucs4", but you can check this way:

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

(We do not support python3.)

For more info on the Python ABI version (and wheel naming conventions): https://github.com/pypa/manylinux

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 your 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} -C ${PREFIX}
export LD_LIBRARY_PATH=${PREFIX}/lib:${LD_LIBRARY_PATH}

userbase

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

Standard

Typically, /usr/local

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

Try it!

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

External dependencies

We require a few extra dependencies. You must install these yourself.

  • mummer-3.3+, for nucmer and show-coords.
  • samtools
  • minimap2

(We no longer require h5py.)

(smrt_bin is no longer needed. These should all be available in your $PATH.)

Problems

Wrong HDF5 version

This can happen if your Python (e.g. Anaconda) selects its own HDF5. You might be able to suppress the warning, but you might have other problems.

(Fortunately we are almost free of HDF5.)

Wrong GLIBC

Use gcc/4.9.2 or later.