HTSeq on Helix
HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays. It is developed by Simon Anders at EMBL Heidelberg.
Example files can be downloaded from http://www-huber.embl.de/users/anders/HTSeq/HTSeq_example_data.tgz.
The environment variable(s) need to be set properly first. The easiest way to do this is by using the modules commands as in the example below.
$ module avail htseq ---------------------- /usr/local/Modules/3.2.9/modulefiles -------------------------------- fhtseq/0.5.3p9(default) $ module load htseq $ module list Currently Loaded Modulefiles:
1) htseq/0.5.3p9 $ module unload htseq $ module show htseq ------------------------------------------------------------------- /usr/local/Modules/3.2.9/modulefiles/htseq/0.5.3p9: module-whatis Sets up htseq 0.5.3p9 prepend-path PYTHONPATH /usr/local/python-2.7/lib prepend-path PATH /usr/local/python-2.7/bin -------------------------------------------------------------------
How To Use
$ module load htseq $ python
Python 2.7.2 (default, Aug 15 2011, 13:51:43)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-51)] on linux2
Type "help", "copyright", "credits" or "license" for more information. >>> import HTSeq
