BigWig manpulation tools using libBigWig and htslib

• cgpBigWig Github Site

• Module Name: cgpbigwig (see the modules page for more information)
• Multithreaded/singlethreaded/MPI...
• This application produces HTML reports. You can use hpcdrive to view these reports on your local workstation.
• Environment variables set
  • cgpBigWig_HOME
• Example files in ???
• Reference data in /fdb/cgpBigWig/

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

[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 cgpbigwig

[user@cn3144 ~]$  

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

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

#!/bin/bash
set -e
module load cgpbigwig
cgpBigWig < cgpBigWig.in > cgpBigWig.out

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] cgpBigWig.sh

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

cgpBigWig < cgpBigWig.in > cgpBigWig.out
cgpBigWig < cgpBigWig.in > cgpBigWig.out
cgpBigWig < cgpBigWig.in > cgpBigWig.out
cgpBigWig < cgpBigWig.in > cgpBigWig.out

Submit this job using the swarm command.

swarm -f cgpBigWig.swarm [-g #] [-t #] --module cgpBigWig