====== RepeatMasker ======
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Currently over 56% of human genomic sequence is identified and masked by the program.

===== Information =====

  * Version: 4.1.2-p1
  * Added: February, 2015
  * Updated: December, 2021
  * Link: http://repeatmasker.org

===== Usage =====

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

Load one version into your environment and run it:
<code>$ module load repeatmasker/4.1.2-p1
$ RepeatMasker</code>

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

<code>$ cd /tmp
$ wget http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.2-p1.tar.gz
$ tar xf RepeatMasker-4.1.2-p1.tar.gz
$ sudo mkdir -p /export/apps/repeatmasker/4.1.2-p1
$ sudo chown aorth:aorth /export/apps/repeatmasker/4.1.2-p1
$ python3 -m venv /export/apps/repeatmasker/4.1.2-p1/venv
$ source /export/apps/repeatmasker/4.1.2-p1/venv/bin/activate
$ cp -r RepeatMasker/* /export/apps/repeatmasker/4.1.2-p1
$ cd /export/apps/repeatmasker/4.1.2-p1
# Here you have to manually enter the paths to trf 4.0.9, hmmer 3.2.1, and rmblast 2.11.0
$ perl ./configure
$ deactivate
$ sudo chown -R root:root /export/apps/repeatmasker/4.1.1</code>