Fast, efficient RNA-Seq metrics for quality control and process optimization.

https://github.com/getzlab/rnaseqc

• Module Name: rnaseqc (see the modules page for more information)
• Example files are under /usr/local/apps/rnaseqc/test_data

Allocate an interactive session and run the interactive job there.

[biowulf]$ sinteractive  --mem=5g
salloc.exe: Granted job allocation 789523
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn0135 are ready for job

[cn0135]$ module load rnaseqc

[cn0135]$ cp -r /usr/local/apps/rnaseqc/test_data /data/$USER/
[cn0135]$ cd /data/$USER/test_data
[cn0135]$ rnaseqc chr1.gtf chr1.bam user.out
[cn0135]$ exit
salloc.exe: Job allocation 789523 has been revoked.

[biowulf]$

1. Create a script file (myscript) similar to the one below

#! /bin/bash
# myscript
set -e

module load rnaseqc || exit 1
cd /data/$USER/test_data
rnaseqc chr1.gtf chr1.bam user.out

2. Submit the script on biowulf:

[biowulf]$ sbatch --mem=5g myscript

Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.

Set up a swarm command file (eg /data/$USER/cmdfile).

cd /data/$USER/dir1; rnaseqc chr1.gtf chr1.bam user.out
cd /data/$USER/dir2; rnaseqc chr1.gtf chr1.bam user.out
cd /data/$USER/dir3; rnaseqc chr1.gtf chr1.bam user.out
...
cd /data/$USER/dir20; rnaseqc chr1.gtf chr1.bam user.out

submit the swarm job:

$ swarm -f cmdfile --module rnaseqc -g 5

For more information regarding running swarm, see swarm.html