Sicer is a clustering approach for identification of enriched domains from histone modification ChIP-Seq data.
Example files can be copied from /usr/local/apps/sicer/1.1/ex
$ module load sicer $ cp -r /usr/local/apps/sicer/1.1/ex /data/$USER/sicer # copy example directory $ cd /data/$USER/sicer $ sh $SICERDIR/SICER.sh /data/$USER/sicer/ test.bed control.bed . hg18 1 200 150 0.74 600 .01
1. Create a script file similar to the lines below.
#!/bin/bash module load sicer cd /data/$USER/sicer sh $SICERDIR/SICER.sh /data/$USER/sicer/ test.bed control.bed . hg18 1 200 150 0.74 600 .01
2. Submit the script on biowulf:
$ sbatch jobscript
For more memory requirement (default 4gb), use --mem flag:
$ sbatch --mem=10g jobscript
Setup a swarm command file:
cd /data/$USER/dir1; sicer command cd /data/$USER/dir2; sicer command cd /data/$USER/dir3; sicer command [......]
Submit the swarm file:
$ swarm -f swarmfile --module sicer
-f: specify the swarmfile name
--module: set environmental variables for each command line in the file
To allocate more memory, use -g flag:
$ swarm -f swarmfile -g 10 --module sicer
-g: allocate more memory
For more information regarding running swarm, see swarm.html
It may be useful for debugging purposes to run jobs interactively. Such jobs should not be run on the Biowulf login node. Instead allocate an interactive node as described below, and run the interactive job there.
biowulf$ sinteractive salloc.exe: Granted job allocation 16535 cn999$ module load sicer cn999$ cd /data/$USER/Examples cn999$ sh $SICERDIR/SICER.sh /data/$USER/sicer/ test.bed control.bed . hg18 1 200 150 0.74 600 .01 cn999$ exit biowulf$
Make sure to exit the job once finished.
If more memory is needed, use --mem flag. For example
biowulf$ sinteractive --mem=10g
