htseq

A framework to process and analyze data from high-throughput sequencing (HTS) assays.

• Version: 0.9.1
• Added: October, 2013
• Updated: September, 2017
• Link: http://htseq.readthedocs.io

See versions of htseq which are available:

$ module avail htseq

Load one version into your environment:

$ module load htseq/0.9.1

Notes from the sysadmin during installation:

$ module load python/3.6.2
$ sudo mkdir -p /export/apps/htseq/0.9.1
$ sudo chown aorth /export/apps/htseq/0.9.1
$ python -m venv /export/apps/htseq/0.9.1
$ . /export/apps/htseq/0.9.1/bin/activate
$ pip install HTSeq
$ pip install matplotlib
$ sudo chown -R root:root /export/apps/htseq/0.9.1

Installation is greatly simplified by using Python 3's built-in venv module to create a dedicated environment, then use standard pip etc to install HTSeq and its dependencies.