INSTALL.md

Installing GenHub

The installation of the GenHub package itself should be pretty painless. The easiest way to install is with pip.

pip install genhub

You can also install directly from the source. Check for the latest stable version on the release listing.

# replace x.y.z with an actual version
wget https://github.com/standage/genhub/archive/x.y.z.tar.gz
tar -xzf x.y.z.tar.gz
cd genhub-x.y.z
python setup.py install

To install the latest unreleased version, pip can install directly from GitHub.

pip install git+https://github.com/standage/genhub.git

All of these methods will also automatically install the pyyaml and pycurl dependencies. See below if you have trouble installing pycurl in a virtual environment.

External software

GenHub is implemented in Python and does not need to be compiled. However, it does depend on a few external software packages that do need to be compiled. The required packages must be installed before you can run GenHub. The optional packages are only required for the specified features.

• required packages
  • the GenomeTools library (installation instructions), version 1.5.8 or higher
  • the AEGeAn Toolkit (installation instructions), version 0.16.0 or higher
    • be sure to run make install-scripts or add AEGeAn's data/scripts/ directory to your $PATH as part of your setup
• optional packages
  • the CD-HIT package (installation instructions), tested with version 4.6.4; required only for the cluster build task
  • the pandas data analysis library (installation instructions); required only for data summary scripts

If installing from source, you can invoke make check from the GenHub root directory to check whether all software prerequisites have been satisfied.

Troubleshooting PycURL installation

On some systems installing the PycURL dependency may require an additional step or two.

• If you are having issues installing PycURL in a virtual environment, try the following workaround: deactivate the virtualenv, install PycURL system-wide (or in a directory you control), and then copy the pycurl files into your virtualenv site-packages.
• If you are on a Fedora machine and lack administrative privileges, you may need to execute export PYCURL_SSL_LIBRARY=nss before installing PycURL. See this page for more information.