HTSbox is a fork of early HTSlib. It is a collection of small experimental tools manipulating HTS-related files. While some of these tools are already part of the official SAMtools package, others are for niche use cases.

• htsbox Main Site

• Module Name: htsbox (see the modules page for more information)
• Multithreaded with the -t flag for certain subcommands.
• Environment variables set
  • HTSBOX_HOME
• Example files in $HTSBOX_HOME/test

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 htsbox

[user@cn3144 ~]$ htsbox abreak -l 0 $HTSBOX_HOME/test/ex3.sam

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

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

#!/bin/bash
set -e
module load htsbox
htsbox abreak -l 0 $HTSBOX_HOME/test/ex3.sam

Submit this job using the Slurm sbatch command.

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

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

htsbox qualbin -t $SLURM_CPUS_PER_TASK -bm7 in1.bam
htsbox qualbin -t $SLURM_CPUS_PER_TASK -bm7 in2.bam
htsbox qualbin -t $SLURM_CPUS_PER_TASK -bm7 in3.bam
htsbox qualbin -t $SLURM_CPUS_PER_TASK -bm7 in4.bam

Submit this job using the swarm command.

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