Difference between revisions of "Psipred"

From Bioinformatikpedia
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<nowiki>#</nowiki> Where the PSIPRED V2 data files have been installed<br>
 
<nowiki>#</nowiki> Where the PSIPRED V2 data files have been installed<br>
 
set datadir = /apps/psipred_3.2/data<br>
 
set datadir = /apps/psipred_3.2/data<br>
  +
<br>
  +
set basename = $1:r<br>
  +
set rootname = `dirname $basename`
  +
  +
<nowiki>#</nowiki> Generate a "unique" temporary filename root<br>
  +
set hostid = `hostid`
  +
set tmproot = psitmp$$$hostid
 
</code>
 
</code>
   
 
Then you should be able to run psipred in /apps/psipred_3.2/:
 
Then you should be able to run psipred in /apps/psipred_3.2/:
 
<code>sudo ./runpsipred <path to your fasta-file></code>
 
<code>sudo ./runpsipred <path to your fasta-file></code>
  +
  +
The results can then be found in the directory /apps/psipred_3.2/
  +
(kind of ugly)

Revision as of 13:08, 24 May 2011

PSIPRED

running locally

Change in /apps/psipred_3.2/runpsipred the following lines:

# The name of the BLAST data bank
set dbname = /data/blast/swiss/uniprot_sprot.fasta

# Where the NCBI programs have been installed
set ncbidir = /apps/blast_old/bin

# Where the PSIPRED V2 programs have been installed
set execdir = /apps/psipred_3.2/src

# Where the PSIPRED V2 data files have been installed
set datadir = /apps/psipred_3.2/data

set basename = $1:r
set rootname = `dirname $basename`

# Generate a "unique" temporary filename root
set hostid = `hostid` set tmproot = psitmp$$$hostid

Then you should be able to run psipred in /apps/psipred_3.2/: sudo ./runpsipred <path to your fasta-file>

The results can then be found in the directory /apps/psipred_3.2/ (kind of ugly)