High-Performance Computing at the NIH
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BRASS on Biowulf

BRASS analyses one or more related BAM files of paired-end sequencing to determine potential rearrangement breakpoints. There are several stages the main component being:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --cpus-per-task=4 --mem=20g
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 BRASS

[user@cn3144 ~]$  brass.pl -c $SLURM_CPUS_PER_TASK -o myout -t tumour.bam -n normal.bam

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

Batch job
Most jobs should be run as batch jobs.

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

#!/bin/bash
set -e
module load BRASS
brass.pl -c $SLURM_CPUS_PER_TASK -o myout -t tumour.bam -n normal.bam

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=4] [--mem=20g] BRASS.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

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

brass.pl -c $SLURM_CPUS_PER_TASK -o myout1 -t tumour1.bam -n normal.bam
brass.pl -c $SLURM_CPUS_PER_TASK -o myout2 -t tumour2.bam -n normal.bam
[...]

Submit this job using the swarm command.

swarm -f BRASS.swarm -g 15 -t 4 --module BRASS
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module BRASS Loads the BRASS module for each subjob in the swarm