Before you start
- To use this setting, your TACC account needs to be allocated to our lab project('A-cm10'). If you don't have an account, create it at https://portal.tacc.utexas.edu/. Then, ask Edward to assign your account as a member of lab project.
- This document is for 'stampede'.
- Currently in most cases I use three search engines: comet, X!Tandem, and MS-GF+.
Install MSblender (and comet, MSGFDB, X!Tandem)
$ cd ~ $ mkdir git $ cd git $ git clone https://github.com/marcottelab/MSblender.git
Prepare a working space
$ module load python $ cd $SCRATCH $ mkdir myProject $ cd myProject $ mkdir mzXML $ mkdir DB $ mkdir comet $ mkdir MSGF+ $ mkdir tandemK
- You can run this process on any computer. If it takes longer than a minute, it would be better to process it on other than TACC login node (your account may be locked).
$ python $HOME/git/MSblender/pre/fasta-reverse.py my_seq.fa $ cat my_seq.fa.* > my_seq.combined.fa
DB setup for X!tandem
$ $HOME/git/MSblender/extern/fasta_pro.exe my_seq.conbind.fa
You may see the message like below:
$ ~/git/MSblender/extern/fasta_pro.exe my_seq.combined.fa fasta_pro file conversion utility, v. 2006.09.15 input path = my_seq.combined.fa output path = my_seq.combined.fa.pro db type = plain
DB setup for comet
You don't need to do anything for this.
DB setup for MSGF+
It uses significant amount of computing resources (i.e. memory), so it may not be suitable to run on login node.
$ module load jdk64 $ java -Xmx4000M -cp /home1/00992/linusben/git/MSblender/extern/MSGFPlus.jar edu.ucsd.msjava.msdbsearch.BuildSA -d XenopusHybrid_xlJGIv16_xtJGIv83.combined.fa -tda 0
Prepare mzXML files
Copy your mzXML files on this diretory ($SCRATCH/myProject/mzXML).