Deeptools on Biowulf
Quick Links
Documentation
Notes
Interactive job
Batch job
Swarm of jobs

deepTools is a suite of user-friendly tools for the visualization, quality control and normalization of data from high-throughput DNA sequencing experiments.

deepTools offers multiple methods for highly-customizable data visualization that immensely aid hypothesis generation and data interpretation. It also offers all the tools needed to create coverage files in standard bedGraph and bigWig file formats allowing various normalization procedures and comparisons between two files (for example, treatment and control).

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 --cpus-per-task=4
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 deeptools
[user@cn3144 ~]$ bamCoverage -b file.bam -o outfile -of bigwig -p $SLURM_CPUS_PER_TASK
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$
$SLURM_CPUS_PER_TASK will be automatically replaced by the number used in the sinteractive command (4 in this example)

Batch job
Most jobs should be run as batch jobs.

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

#!/bin/bash
set -e
module load deeptools
bamCoverage -b file.bam -o outfile -of bigwig -p $SLURM_CPUS_PER_TASK

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 --mem=10g deeptools.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. deeptools.swarm). For example:

cd dir1; bamCoverage -b file.bam -o outfile -of bigwig -p $SLURM_CPUS_PER_TASK
cd dir2; bamCoverage -b file.bam -o outfile -of bigwig -p $SLURM_CPUS_PER_TASK
cd dir3; bamCoverage -b file.bam -o outfile -of bigwig -p $SLURM_CPUS_PER_TASK
cd dir4; bamCoverage -b file.bam -o outfile -of bigwig -p $SLURM_CPUS_PER_TASK

Submit this job using the swarm command.

swarm -f deeptools.swarm g 10 t 4 --module deeptools
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 Loads the module for each subjob in the swarm