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.
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.
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.