RapMap

Overview

RapMap is a testing ground for ideas in lightweight / quasi / pseudo transcriptome alignment.

Version 0.1.0 is installed on the CSF.

Restrictions on use

Open source, may be used by all CSF users.

Set up procedure

To access the software you must first load the modulefile:

module load apps/gcc/rapmap/0.1.0

Running the application

Please do not run RapMap on the login node. Jobs should be submitted to the compute nodes via batch.

Serial batch job submission – details coming soon

Make sure you have the modulefile loaded then create a batch submission script, for example:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd             # Job will run from the current directory
#$ -V               # Job will inherit current environment settings

APP arg1 arg2 > out.log

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Further info

• https://github.com/COMBINE-lab/RapMap

Updates

None.