HMMRATAC
Overview
HMMRATAC peak caller for ATAC-seq data
Version 1.2.5 is installed on the CSF.
Restrictions on use
This software is open source and may be used by anyone on the CSF.
Set up procedure
We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.
Load one of the following modulefiles:
module load apps/binapps/hmmratac/1.2.5
Running the application
Please do not run hmmratac on the login node. Jobs should be submitted to the compute nodes via batch.
On a desktop system you would call use java -jar HMMRATAC_V1.2.5_exe.jar to execute the software. On the CSF because it is centrally installed and the path to it is quite long we have written a small script which does this part for you so you simply use the command
hmmratac
with the options and input files you then require. See below jobscript for a more detailed example.
Serial batch job submission
Create a batch submission script (which will load the modulefile in the jobscript), for example:
#!/bin/bash --login #$ -cwd # Job will run from the current directory # NO -V line - we load modulefiles in the jobscript module load apps/binapps/hmmratac/1.2.5 hmmratac -b SortedBAM -i BAMIndex -g GenomeStatsFile options
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.