Python Modules
The default Python distribution for BioITeam members on TACC is the 2.7.2 Enthought distribution. This includes a plethora of packages beyond the standard set, including SciPy, NumPy and Biopython. The ordinary TACC Python default is an earlier version of Python, but a special .profile setting for BioITeam members automatically loads the newer TACC module for Python (2.7.2), along with the Enthought distribution.
Importing Non-Standard Python Modules
Python modules that are not part of the Enthought distribution are in a special directory on Corral:
/corral-repl/utexas/BioITeam/python2.7/site-packages
If you are using the standard BioITeam profile (or at least including it), your PYTHONPATH environment variable is set so that you can load Python modules in this special directory in the usual way. To load "my_special_module" in our special Corral directory, just run
import my_special_module
as usual.
Installing Non-Standard Python Modules
Installing new Python modules in TACC can be a little bit tricky. The standard Python package installers like setup.py or easy_install will try to install into the default TACC Python directory, which we don't have permissions for. Various installers have options to specify a custom installation directory. ed: I am not 100% sure these flags work.
Using setup.py
Navigate into the package directory and use the --prefix flag, for example:
python setup.py install --prefix=/corral-repl/utexas/BioITeam/python2.7/site-packages
Using easy_install
Try easy_install as usual, but use the --install-dir=DIR flag, so you would type something like:
easy_install --install-dir=/corral-repl/utexas/BioITeam/python2.7/site-packages <my_new_awesome_python_package>