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pear-software

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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

Usage

See which versions of pear are available:

$ module avail pear

Load one version into your environment and run it:

$ module load pear/0.9.6
$ pear

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:

$ 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

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.

pear-software.txt · Last modified: 2020/04/16 14:14 by aorth