Biowulf High Performance Computing at the NIH
Rscape on Biowulf

R-scape looks for evidence of a conserved RNA structure by measuring pairwise covariations observed in an input multiple sequence alignment. It analyzes all possible pairs, including those in your proposed structure (if you provide one). R-scape uses a null hypothesis that takes phylogenetic correlations and base composition biases into account, which can be sources of apparent pairwise covariation that are not due to conserved RNA structure.

Documentation

http://eddylab.org/R-scape/

Important Notes
Submitting an interactive job

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]$ cd /data/$USER/

[cn0135]$ module load rscape

[cn0135]$ cp -rp /usr/local/apps/rscape/1.5.2/tutorial .
[cn0135]$ cd tutorial
[cn0135]$ R-scape -s updated_Arisong.sto

[cn0135]$ exit
salloc.exe: Job allocation 789523 has been revoked.

Submitting a single batch job

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

#! /bin/bash
# myscript
set -e

module load rscape || exit 1
cd /data/$USER/tutorial
R-scape -s updated_Arisong.sto

2. Submit the script on biowulf:

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

Using Swarm

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/$USER/dir1; R-scape -s updated_Arisong.sto
cd /data/$USER/dir2; R-scape -s updated_Arisong.sto
cd /data/$USER/dir3; R-scape -s updated_Arisong.sto
...
cd /data/$USER/dir20; R-scape -s updated_Arisong.sto

submit the swarm job:

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

For more information regarding running swarm, see swarm.html