weblogo on Biowulf2 & Helix

The weblogo package includes a tool ( seqlogo) to generate sequence logos from aligned sequences in fastq format.

Note that weblogo changed significantly from version 2.X to 3.X. The commands listed here are for versions 3.X



Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cann ot be run as batch jobs.

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 weblogo
[+] Loading weblogo 3.6
[user@cn3144 ~]$ cp $WEBLOGO_DATA/* .
[user@cn3144 ~]$ weblogo -f ctcf.fa -F png -o ctcf.png

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$
Visualization of the output image ctcf.png:
Batch job on Biowulf2
Most jobs should be run as batch jobs.

Create a batch script similar to the following example:

#! /bin/bash
#SBATCH --mem=100m
#SBATCH --time=5
# this file is seqlogo_job.sh

module load weblogo || exit 1
weblogo -f ctcf.fa -F png -o ctcf.png

Submit to the queue with sbatch:

biowulf$ sbatch seqlogo_job.sh
Swarm of jobs on Biowulf2
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarm command file similar to the following example:

# this file is seqlogo_jobs.swarm
seqlogo -f site1.fa -F eps -o site1 -abcMnY
seqlogo -f site2.fa -F eps -o site2 -abcMnY
seqlogo -f site3.fa -F eps -o site3 -abcMnY
seqlogo -f site4.fa -F eps -o site4 -abcMnY

And submit to the queue with swarm

biowulf$ swarm -f seqlogo_jobs.swarm --time=5