Biowulf High Performance Computing at the NIH
Bedops on Biowulf

Bedops is a software package for manipulating and analyzing genomic interval data. It contains tools to

Operations can be parallelized efficiently by chromosome.

Each tool is designed to use unix input and output streams for building efficient pipelines.


Shane Neph, et al. BEDOPS: high-performance genomic feature operations Bioinformatics 2012, 28:1919-1920. Pubmed |  PMC |  Journal

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 ~]$ convert2bed --input=bam --output=starch --starch-note "wt/H3ac/a13" < bam_inputfile > starch/a13.starch
[user@cn3144 ~]$ unstarch --note starch/a13.starch wt/H3ac/a13
[user@cn3144 ~]$ unstarch --elements starch/a13.starch
[user@cn3144 ~]$ unstarch --bases-uniq starch/a13.starch

[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. For example:

set -e
module load bedops
sort-bed in.bed > out.bed

Submit this job using the Slurm sbatch command.

sbatch [--mem=#]
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. bedops.swarm). For example:

cd dir1; sort-bed in.bed > out.bed
cd dir2; sort-bed in.bed > out.bed
cd dir3; sort-bed in.bed > out.bed
cd dir4; sort-bed in.bed > out.bed

Submit this job using the swarm command.

swarm -f bedops.swarm [-g #] --module bedops
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module Loads the module for each subjob in the swarm