Difference between revisions of "MSblender TACC"

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(DB setup for MSGFDB)
(DB setup for X!tandem)
Line 65: Line 65:
  input path = XENLA_prot_v4_combined.fasta
  input path = XENLA_prot_v4_combined.fasta
output path = XENLA_prot_v4_combined.fasta.pro
output path = XENLA_prot_v4_combined.fasta.pro
db type = plain
db type = plain</pre>
=== DB setup for Crux ===
=== DB setup for Crux ===

Revision as of 12:31, 14 February 2012


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.
  • Generally, 'longhorn' has shorter queue than 'lonestar'. So if you don't need large memory(> 4GB), use 'longhorn'.
  • Always work at $SCRATCH directory, not at /corral or your $HOME.
  • All source codes are available at /corral/utexas/A-cm10/src.MS/. Personally I use symbolic link for this directory under $HOME so I can use '~' shortcut.
$ ln -s /corral/utexas/A-cm10/src.MS/ ~/src.MS 
$ ls ~/src.MS 
  • All packages are installed at /corral/utexas/A-cm10/src.MS/local/.
  • To run InsPecT, you need to set LD_LIBRARY_PATH for expat library. Type below command before running InsPecT (or put it on '$HOME/.profile_user'
 $ export LD_LIBRARY_PATH="/corral/utexas/A-cm10/src.MS/local/lib/" 
  • Default python interpreter is 2.4 at TACC. You need to load 2.7.1 as below.
 $ module load python

Currently installed packages

These packages are installed at lonestar.

  • TPP-4.5.1 + X!Tandem (2010.10.01.1)
  • /corral/utexas/A-cm10/src.MS/local/tppbin/xinteract (integrated wrapper for *Prophet)
  • /corral/utexas/A-cm10/src.MS/local/tppbin/tandem (X!Tandem with k-score support)
  • Crux 1.37
    • /corral/utexas/A-cm10/src.MS/local/bin/crux
  • Tide 1.0
    • /corral/utexas/A-cm10/src.MS/local/bin/tide-index
    • /corral/utexas/A-cm10/src.MS/local/bin/tide-msconvert
    • /corral/utexas/A-cm10/src.MS/local/bin/tide-search
  • MSGFDB (20120106)
    • /corral/utexas/A-cm10/src.MS/MSGFDB/current/MSGFDB.jar
  • InsPecT (20120109)
    • /corral/utexas/A-cm10/src.MS/local/bin/inspect

Install MS-toolbox & MSblender

  • I recommend to install MS-toolbox at your home individually, because everyone may want to use different search parameters.
$ module load git
$ cd ~
$ mkdir git
$ cd git
$ git clone git@github.com:marcottelab/MS-toolbox.git
$ git clone git@github.com:marcottelab/MSblender.git
  • You don't need to compile MSblender codes under 'src' directory. Executable file is already available at /corral/utexas/A-cm10/src.MS/local/bin/msblender.

Let's start

$ module load python
$ mkdir my-project
$ cd my-project
$ python ~/git/MS-toolbox/bin/mstb-setup.py

It will make five directories (DB, mzXML, RAW, scripts, tmp), and one text file called 'mstb.conf'. Transfer your mzXML files to 'mzXML' directory. I also keep RAW files on the same directory. But it would be good to transfer them to corral & ranch(tape storage) to archive.

Setup your database

Transfer your FASTA file to 'DB' directory. You need 'combined' database, with target and decoy. It is recommended to use 'reverse' decoy sequences. If you use 'fasta-reverse.py' script on MS-toolbox, it generates reverse sequence with 'rv_'prefix.

$ python ~/git/MS-toolbox/bin/fasta-reverse.py XENLA_prot_v4.fasta 
$ mv XENLA_prot_v4.fasta.target XENLA_prot_v4_combined.fasta
$ cat XENLA_prot_v4.fasta.reverse >> XENLA_prot_v4_combined.fasta
$ head -n 1 XENLA_prot_v4.fasta
$ head -n 1 XENLA_prot_v4.fasta.reverse 

DB setup for X!tandem

 $~/src.MS/local/bin/fasta_pro.exe (my combined fasta file) 

It makes an index file with '.pro' suffix after your FASTA filename.

 $~/src.MS/local/bin/fasta_pro.exe XENLA_prot_v4_combined.fasta 
fasta_pro file conversion utility, v. 2006.09.15
 input path = XENLA_prot_v4_combined.fasta
output path = XENLA_prot_v4_combined.fasta.pro
db type = plain

DB setup for Crux

 $~/src.MS/local/bin/crux create-index --enzyme trypsin --missed-cleavages 2 --peptide-list T --decoys none (my combined fasta file) (my index name)
  • If you want to use Crux function separately (or other embeded post-processing tool, i.e. percolator or q-ranker), you should use FASTA file with target sequence only, with certain decoy option (default option is protein-shuffle, but peptide-shuffle would be better.)
  • 'peptide-list' is optional.
  • Trypsin digestion pattern in Crux is '[KR]|{P}', so it does not cut K/R if the next AA is P. If you want to ignore this 'Proline' constraint, you can use '--custom-enzyme "[KR]|[X]"' instead of '--enzyme trypsin'.

DB setup for InsPecT

 $~/src.MS/inspect/current/PrepDB.py FASTA (my fasta file)
  • It makes an index file with '.trie' suffix after your FASTA filename.

DB setup for MSGFDB

$ java -cp ~/src.MS/MSGFDB/current/MSGFDB.jar msdbsearch.BuildSA -d (my FASTA file) -tda 0
  • It generates .canno, .cnlcp, .csarr & .cseq files.
  • If you want to use native MS-GFDB function, use -tda 2 (generate target & combined database) with target-only FASTA file.