ILRI Research Computing

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====== hic_qc ======
This script is intended as a simple QC method for Hi-C libraries, based on reads in a BAM file aligned to some genome/assembly.

===== Information =====

  * Version: git-1e132fb2
  * Added: November, 2020
  * Link: https://github.com/phasegenomics/hic_qc

===== Usage =====

See versions of hic_qc that are available:
<code>$ module avail hic_qc</code>

Load one version into your environment and run it:
<code>$ module load hic_qc/git-1e132fb2
$ hic_qc.py</code>

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

<code>$ cd /tmp
$ git clone https://github.com/phasegenomics/hic_qc.git
$ cd hic_qc
$ sudo mkdir -p /export/apps/hic_qc/git-1e132fb2
$ sudo chown aorth /export/apps/hic_qc/git-1e132fb2
$ python3 -m venv /export/apps/hic_qc/git-1e132fb2
$ source /export/apps/hic_qc/git-1e132fb2/bin/activate
$ pip install -r requirements.txt
$ python setup.py install
$ cp -r * /export/apps/hic_qc/git-1e132fb2
$ sudo chown -R root:root /export/apps/hic_qc/git-1e132fb2</code>