Useq on Helix
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.
Programs location
/usr/local/useq/
The environment for USeq can be set up with the 'module load useq' command. This will also set up the following environment variables:$USEQ - points to the USeq applications area
$USEQDOCS - points to the USeq documentation
Command-line usage
$ java -jar -Xmx#G $USEQ/Appchoice
For example, to run the USeq program ChIPSeq using 8 GB of memory, you would type:
java -jar -Xmx8G $USEQ/ChIPSeq
To Run GUI Interface
First log in to Helix with an Xwindows connection
The first time you run the USeq GUI, you will need to create a directory called /home/username/.GWrap and link the USeq applications and documentation as in the example below:[user@helix ~]$ cd /data/YourUserID [user@helix ~]$ module load useq [user@helix ~]$ mkdir ~/.GWrap [user@helix ~]$ ln -s $USEQ ~/.GWrap/Apps [user@helix ~]$ ln -s $USEQDOCS ~/.GWrap/Documentation [user@helix ~]$ 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...]
