'UNSW - Science

UNSW - Science - HPC

BioPython 1.65

Summary

Python 2.7.9 with Biopython 1.65 is installed in /share/apps/python/2.7.9

This version of Python is independent of the system version of Python and includes a number of modules such as Biopython 1.65, NumPy 1.9.2, SciPy 0.15.1 and IPython 3.1.0

You should use this module or another Python module where Python is used for compute jobs to ensure that your jobs are not affected by updates to the system version of Python.

To make sure that your Python code uses the version of Python that you have loaded using the module command your Python file should begin with

#!/usr/bin/env python
rather than pointing directly at the Python executable.

If you wish to install additional Python modules you should set up your virtual environment using the virtualenv command and then use the pip command which allows you to install modules for your own use. Information on using pip is available by typing

pip --help
or online at https://pip.pypa.io/en/latest/quickstart.html.

More information about the commands made available by this module is available by typing
man python
or online at http://www.python.org. Information on Biopython is available at http://www.biopython.org.

Group

BioPython 1.65 is part of the bio collection of software.

Conflicts

BioPython 1.65 conflicts with the following modules and will not load if any of them is already loaded.

Location

BioPython 1.65 is installed in /share/apps/python/2.7.9.

Manual Pages

After you have loaded BioPython 1.65, you will be able to use the man command for details on how the loaded commands work.

Paths

When loaded, BioPython 1.65 will add the following paths to your environment.

Variable
Path
PATH
/share/apps/python/2.7.9/bin
LD_LIBRARY_PATH
/share/apps/python/2.7.9/lib
CPATH
/share/apps/python/2.7.9/include
LIBRARY_PATH
/share/apps/python/2.7.9/lib
MANPATH
/share/apps/python/2.7.9/share/man