ILRI Research Computing

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

===== Information =====

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

===== Usage =====

See versions of htseq which are available:
<code>$ module avail htseq</code>

Load one version into your environment:
<code>$ module load htseq/0.9.1</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ 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</code>

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.