====== PEAR ======

An ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.

===== Information =====

  * Version: 0.9.6
  * Added: September, 2016
  * Updated: April, 2020
  * Link: https://www.h-its.org/software/pear-paired-end-read-merger/

===== Usage =====

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

Load one version into your environment and run it:
<code>$ module load pear/0.9.6
$ pear</code>

Note: please use the ''-j'' option to control how many CPU threads pear uses. This should match the number of CPUs you requested in your SLURM SBATCH job parameters.

===== Installation ======

Notes from the sysadmin during installation:

<code>
$ cd /tmp
$ wget https://depot.galaxyproject.org/software/pear/pear_0.9.6_src_all.tar.gz
$ tar xf pear_0.9.6_src_all.tar.gz
$ cd pear-0.9.6-src
$ scl enable devtoolset-7 bash
$ ./configure --prefix=/export/apps/pear/0.9.6
$ make
$ sudo mkdir -p /export/apps/pear/0.9.6
$ sudo chown aorth /export/apps/pear/0.9.6
$ make install
$ sudo chown -R root:root /export/apps/pear/0.9.6
</code>

Note: I downloaded this from galaxyproject because the upstream site requires academic registration and I never received the confirmation mail to download the software. Also, this is the URL that is used by Conda.