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

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

Example:

• https://downloads.pacbcloud.com/public/falcon/falcon-2018.08.08-21.41-py2.7-ucs4-beta.tar.gz

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.

• https://github.com/PacificBiosciences/FALCON_unzip/issues/83

(Fortunately we are almost free of HDF5.)

Wrong GLIBC

Use gcc/4.9.2 or later.