USEQ on Biowulf

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USeq on Biowulf

USeq is a collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms. Initial emphasis: chIP-seq and RNA-Seq with FDR estimations. USeq is under continuous development at the Huntsman Cancer Institute in the Utah Bioinformatics Shared Resource Center.

USeq requires the R program. The appropriate paths can be set up with the 'module load useq' command. This module also sets an environment variable called $USEQ that points to the location of the USeq jar files, and $USEQDOCS that point to the documentation.

Programs Location

/usr/local/useq/Apps

Submitting a single USeq batch job

1. Create a script file. The file will contain the lines similar to the lines below.

#!/bin/bash
# This file is runUseq
#
#PBS -N Useq
#PBS -m be
#PBS -k oe

module load useq

cd /data/user/mydir
java -jar $USEQ/Gr2Bar -f /data/user/myseqs/ -v hg19

3. Submit the script using the 'qsub' command on Biowulf:

qsub -l nodes=1 runUseq

Submitting a swarm of Useq jobs

Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.

Set up a swarm command file (eg /data/username/cmdfile). Here is a sample file:

module load useq; cd /data/user/myseqs; java -jar $USEQ/SamParser -v hg19 -f /data/user/myseqs1
module load useq; cd /data/user/myseqs; java -jar $USEQ/SamParser -v hg19 -f /data/user/myseqs2
[...]

Submit this swarm with:

swarm -g # -f cmdfile

where '#' represents the amount of memory required by a single command in the file above. The USeq documentation provides some clues about memory usage. For example, the USeq ChIPSeq program requires 6-8 GB RAM. If you were running a swarm of ChIPSeq jobs that each required 8 GB of memory, you would submit with:

swarm -g 8 -f cmdfile

For more information regarding running swarm, see swarm.html

To Run USeq GUI Interface

You can also run the GUI on Helix.

First log in to biowulf with an Xwindows connection and request an interactive node with '-V' flag. DO NOT RUN THIS ON BIOWULF HEAD NODE.

The first time you run the USeq GUI, you will need to create a directory called /home/username/.GWrap and link the USeq applications and documentation as in the example below:

$ qsub -I -l nodes=1
qsub: waiting for job 2407235.biobos to start
qsub: job 2407235.biobos ready

[user@p480 ~]$ cd /data/YourUserID

[user@p480 ~]$ module load useq

[user@p480 ~]$ mkdir ~/.GWrap
[user@p480 ~]$ ln -s $USEQDOCS ~/.GWrap/Apps
[user@p480 ~]$ ln -s $USEQDOCS ~/.GWrap/Documentation

[user@biowulf ~]$ java -jar $USEQ/GWrap_GUI_ClickMe.jar 
Here findDirectories()
Looking for dirs in /home/user
Attempting to get them from webstart jar file.
Attempting to pull files using copyDocsApps()
src jar /usr/local/USeq_8.3.4/LibraryJars/bioToolsCodeLibrary.jar
Making prefs dialog
Adding Apps menu items /home/user/.GWrap/Apps
ABITraceTCPeakCalculator
AggregatePlotter
Alleler
AllelicMethylationDetector
[...etc...]

Documentation

http://useq.sourceforge.net/