| The CSF2 has been replaced by the CSF3 - please use that system! This documentation may be out of date. Please read the CSF3 documentation instead. To display this old CSF2 page click here. |
X! Tandem
Overview
X! Tandem is open source software that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identification.
Version 13-09-01-1 (SLEDGEHAMMER) is installed on the CSF. It was compiled with gcc 4.4.6 .
Restrictions on use
this software is open source, all users may use it.
Set up procedure
To access the software you must first load the modulefile:
module load apps/gcc/xtandem/1309011
Running the application
Please do not run X! Tandem on the login node. Jobs should be submitted to the compute nodes via batch.
Serial batch job submission
Make sure you have the modulefile loaded.
Create a directory with all the files required for your job run – e.g. your fast files, and an xml input file which describes where the fasta files are and the parameters for the search.
Then create a batch submission script in the same directory, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings tandem.exe input.xml
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Parallel batch job submission
X! Tandem cannot run parallel jobs. We strongly recommend the use of SGE Job Arrays for running multiple serial jobs.
Further info
Updates
None.