PyCogent is a software library for genomic biology.

http://pycogent.sourceforge.net/

Installation Directory

BASE = /sw/python/2.7.1/lib/python2.7/site-packages

cogent
cogent-1.5.1-py2.7.egg-info

 module load python/2.7.1 

Installation

http://pycogent.sourceforge.net/install.html#installing-easy-install

/usr/local/src/pycogent

module load python/2.7.1
Download the requirements file.
wget http://pycogent.sourceforge.net/_downloads/cogent-requirements.txt

Install pip
easy_install -U pip

Use pip to download, build and install PyCogent plus the numpy dependency

DONT_USE_PYREX=1 sudo pip install -r /usr/local/src/pycogent/cogent-requirements.txt

http://pycogent.sourceforge.net/README.html

PyCogent/tests contains all the tests (currently >3100). You can most readily run the tests using the PyCogent/run_tests shell script. This is done by typing:

sh run_tests   

module load python/2.7.1
sh /sw/pycogent/PyCogent-1.5.1/run_tests

Ran 3668 tests in 97.640s

FAILED (failures=7, errors=4)