Difference between revisions of "Psipred"
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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> |
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set datadir = /apps/psipred_3.2/data<br> |
set datadir = /apps/psipred_3.2/data<br> |
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+ | <br> |
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+ | set basename = $1:r<br> |
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+ | set rootname = `dirname $basename` |
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+ | |||
+ | <nowiki>#</nowiki> Generate a "unique" temporary filename root<br> |
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+ | set hostid = `hostid` |
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+ | set tmproot = psitmp$$$hostid |
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</code> |
</code> |
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Then you should be able to run psipred in /apps/psipred_3.2/: |
Then you should be able to run psipred in /apps/psipred_3.2/: |
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<code>sudo ./runpsipred <path to your fasta-file></code> |
<code>sudo ./runpsipred <path to your fasta-file></code> |
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+ | |||
+ | The results can then be found in the directory /apps/psipred_3.2/ |
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+ | (kind of ugly) |
Revision as of 13:08, 24 May 2011
PSIPRED
running locally
Change in /apps/psipred_3.2/runpsipred the following lines:
# The name of the BLAST data bank
set dbname = /data/blast/swiss/uniprot_sprot.fasta
# Where the NCBI programs have been installed
set ncbidir = /apps/blast_old/bin
# Where the PSIPRED V2 programs have been installed
set execdir = /apps/psipred_3.2/src
# Where the PSIPRED V2 data files have been installed
set datadir = /apps/psipred_3.2/data
set basename = $1:r
set rootname = `dirname $basename`
# Generate a "unique" temporary filename root
set hostid = `hostid`
set tmproot = psitmp$$$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)