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SICER on Biowulf & Helix

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

Running on Helix
$ 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

Running a single batch job on Biowulf

1. Create a script file similar to the lines below.


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

Running a swarm of jobs on Biowulf

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

Running an interactive job on Biowulf

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


Make sure to exit the job once finished.

If more memory is needed, use --mem flag. For example

biowulf$ sinteractive --mem=10g