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Integrative on Biowulf & Helix


Software Pipeline for Integrative Genetic Association Analysis: Probabilistic Assessment of Enrichment and Colocalization

There may be multiple versions available on our systems. An easy way of selecting the version is to use modules. To see the modules available, type

module avail integrative 

To select a module use

module load integrative/[version]

where [version] is the version of choice.

Environment variables set


Interactive job on Biowulf

Allocate an interactive session with sinteractive and use as described below

biowulf$ sinteractive --mem=5g
salloc.exe: Pending job allocation 38978697
salloc.exe: Nodes cn2273 are ready for job
node$ module load integrative
[+] Loading integrative
node$ dap-g -d gene_name.dat -scan > gene_name.bf
node$ exit


Batch job on Biowulf

Create a batch script similar to the following example:

#! /bin/bash
# this file is integrative.batch

module load integrative || exit 1
cd /data/$USER
dap-g -d gene_name.dat -scan > gene_name.bf

Submit to the queue with sbatch:

biowulf$ sbatch integrative.batch


Swarm of Jobs on Biowulf

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

# this file is called script.swarm
cd dir1; integrative command 1;integrative command 2
cd dir2; integrative command 1; integrative command 2
cd dir3; integrative command 1; integrative command 2

Submit this job using the swarm command.

swarm -f script.swarm --module integrative

For more information regarding swarm: https://hpc.nih.gov/apps/swarm.html#usage