{"id":2395,"date":"2015-04-10T08:08:25","date_gmt":"2015-04-10T08:08:25","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=2395"},"modified":"2015-04-10T08:59:36","modified_gmt":"2015-04-10T08:59:36","slug":"xtandem","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/xtandem\/","title":{"rendered":"X! Tandem"},"content":{"rendered":"

Overview<\/h2>\n

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.<\/p>\n

Version 13-09-01-1 (SLEDGEHAMMER) is installed on the CSF. It was compiled with gcc 4.4.6 .<\/p>\n

Restrictions on use<\/h2>\n

this software is open source, all users may use it. <\/p>\n

Set up procedure<\/h2>\n

To access the software you must first load the modulefile:<\/p>\n

\r\nmodule load apps\/gcc\/xtandem\/1309011\r\n<\/pre>\n
Running the application<\/h2>\n
Please do not run X! Tandem on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n
Serial batch job submission<\/h3>\n
Make sure you have the modulefile loaded.<\/p>\n
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.<\/p>\n
Then create a batch submission script in the same directory, for example:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n\r\ntandem.exe input.xml\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Parallel batch job submission<\/h3>\n
X! Tandem cannot run parallel jobs. We strongly recommend the use of SGE Job Arrays<\/a> for running multiple serial jobs.<\/p>\n
Further info<\/h2>\n