Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data developed by the Bioinformatics Laboratory of Institut Curie (Paris).

• https://github.com/BoevaLab/FREEC

• Module Name: freec (see the modules page for more information)
• Example files in /usr/local/apps/freec/test.zip

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 freec
[user@cn3144 ~]$ freec -conf config_ctrl.txt

[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 freec
freec -conf config_ctrl.txt

Submit this job using the Slurm sbatch command.

sbatch batch.sh

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

cd dir1; freec -conf config_ctrl.txt
cd dir2; freec -conf config_ctrl.txt
cd dir3; freec -conf config_ctrl.txt

Submit this job using the swarm command.

swarm -f job.swarm --module freec