Quick Links Documentation Notes Interactive job Batch job Swarm of jobs

Sicer is a clustering approach for identification of enriched domains from histone modification ChIP-Seq data

 

• https://home.gwu.edu/~wpeng/Software.htm

• Module Name: SICER (see the modules page for more information)
• environment variables set
  • SICERDIR
• Example files in /usr/local/apps/sicer/1.1/ex

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load sicer
[user@cn3144 ~]$ cd /data/$USER/sicer
[user@cn3144 ~]$ sh $SICERDIR/SICER.sh /data/$USER/sicer/ test.bed control.bed . hg18 1 200 150 0.74 600 .01

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. batch.sh). For example:

#!/bin/bash
set -e
module load sicer
sh $SICERDIR/SICER.sh /data/$USER/sicer/ test.bed control.bed . hg18 1 200 150 0.74 600 .01

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] batch.sh

Create a swarmfile (e.g. job.swarm). For example:

cd dir1; sh $SICERDIR/SICER.sh /data/$USER/sicer/ test.bed control.bed . hg18 1 200 150 0.74 600 .01
cd dir2; sh $SICERDIR/SICER.sh /data/$USER/sicer/ test.bed control.bed . hg18 1 200 150 0.74 600 .01
cd dir3; sh $SICERDIR/SICER.sh /data/$USER/sicer/ test.bed control.bed . hg18 1 200 150 0.74 600 .01

Submit this job using the swarm command.

swarm -f job.swarm [-g #] --module sicer

where

-g #	Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module	Loads the module for each subjob in the swarm