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Control-FREEC on Biowulf and Helix

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).

The test data can be copied : /usr/local/apps/freec/test.zip

Running on Helix

Sample session:

helix$ module load freec
helix$ freec -conf config_ctrl.txt

Submitting a single batch job

1. Create a script file. The file will contain the lines similar to the lines below.

#!/bin/bash 

module load freec
cd /data/$USER/somewhere
freec -conf config_ctrl.txt
....
....

2. Submit the script on Biowulf.

$ sbatch myscript

see biowulf user guide for more options such as allocate more memory and longer walltime.

Submitting a swarm of jobs

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). Here is a sample file:

cd /data/user/run1/; freec -conf config_ctrl.txt
cd /data/user/run2/; freec -conf config_ctrl.txt
cd /data/user/run3/; freec -conf config_ctrl.txt
........

The -f flag is required to specify swarm file name.

Submit the swarm job:

$ swarm -f swarmfile --module freec

- Use -g flag for more memory requirement (default 1.5gb per line in swarmfile)

- Use --time flag for longer walltime (default 4 hours)

For more information regarding running swarm, see swarm.html

 

Running an interactive job

User may need to run jobs interactively sometimes. 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.

[user@biowulf]$ sinteractive 

[user@pXXXX]$ cd /data/$USER/myruns

[user@pXXXX]$ module load freec

[user@pXXXX]$ freec -conf config_ctrl.txt
[user@pXXXX] exit
slurm stepepilog here!
                   
[user@biowulf]$ 

Documentation

http://bioinfo-out.curie.fr/projects/freec/tutorial.html#Example