Biowulf High Performance Computing at the NIH
MAGMA on Biowulf

MAGMA is a tool for gene analysis and generalized gene-set analysis of GWAS data. It can be used to analyse both raw genotype data as well as summary SNP p-values from a previous GWAS or meta-analysis.

References:

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@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 MAGMA

[user@cn3144 ~]$ magma --annotate --snp-loc /usr/local/apps/MAGMA/gene_location/example.snp.txt \
--gene-loc /usr/local/apps/MAGMA/gene_location/NCBI37.3/NCBI37.3.gene.loc \
--out temp.test

[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. MAGMA.sh). For example:

#!/bin/bash
module load MAGMA
magma --annotate --snp-loc /usr/local/apps/MAGMA/gene_location/example.snp.txt \
--gene-loc /usr/local/apps/MAGMA/gene_location/NCBI37.3/NCBI37.3.gene.loc \
--out temp.test

Submit this job using the Slurm sbatch command.

sbatch MAGMA.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. MAGMA.swarm). For example:

magma annotate --snp-loc snp1.txt --gene-loc NCBI37.3.gene.loc --out out1
magma annotate --snp-loc snp2.txt --gene-loc NCBI37.3.gene.loc --out out2
magma annotate --snp-loc snp3.txt --gene-loc NCBI37.3.gene.loc --out out3

Submit this job using the swarm command.

swarm -f MAGMA.swarm [-g #] [-t #] --module MAGMA
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 MAGMA Loads the MAGMA module for each subjob in the swarm