SignalIP-Sapelo2: Difference between revisions

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[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===


Bioinformatics
=== Program On ===
Sapelo2
=== Version ===
4.1f
=== Author / Distributor ===
[http://www.cbs.dtu.dk/services/SignalP SignalP]
=== Description ===
"SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes.".
More details are at [http://www.cbs.dtu.dk/services/SignalP SignalP]
=== Running Program ===
Also refer to [[Running Jobs on Sapelo2]]
For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.
*Version 4.1f, installed in /usr/local/apps/eb/SignalP/4.1f-foss-2016b.
To use this version of SignalP, please first load the module with
<pre class="gscript">
ml SignalP/4.1f-foss-2016b
</pre>
Sample job submission script (sub.sh) to run SignalP in a batch job:
<pre class="gscript">
#PBS -S /bin/bash
#PBS -N j_SignalP
#PBS -q batch
#PBS -l nodes=1:ppn=1:AMD
#PBS -l walltime=480:00:00
#PBS -l mem=10gb
cd $PBS_O_WORKDIR
ml SignalP/4.1f-foss-2016b
time signalp [options]
</pre>
where [options] need to be replaced by the options (command and arguments) you want to use.  Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of nodes and cores per node, and the job name need to be modified appropriately as well.
Example of job submission
<pre  class="gcommand">
qsub  sub.sh
</pre>
=== Documentation ===
<pre  class="gcommand">
ml SignalP/4.1f-foss-2016b
signalp -h
  Description: Predict signal peptide and cleavage site.
  Usage: /usr/local/apps/eb/SignalP/4.1f-foss-2016b/signalp -f <format>  -p <graphics-type> -k -s <networks> -t <organism-type> -m <fasta-file> -n <gff-file> -v -l <logfile> -u <value>  -U <value> -w -h -c <value> -T <temp dir> -V <fasta-file(s)>
  Options:
  -f  Setting the output format ('short', 'long', 'summary' or 'all'). Default: 'short'
  -g  Graphics 'png' or 'png+eps'. Default: 'Off'
  -k  Keep temporary directory. Default: 'Off'
  -s  Signal peptide networks to use ('best' or 'notm'). Default: 'best'
  -t  Organism type> (euk, gram+, gram-). Default: 'euk'
  -m  Make fasta file with mature sequence. Default: 'Off'
  -n  Make gff file of processed sequences. Default: 'Off'
  -T  Specify temporary file directory. Default: /usr/local/apps/tmp/SignalP-4.1f-foss-2016b
  -w  web predictions. Default: 'Off'
  -u  user defined D-cutoff for noTM networks
  -U  user defined D-cutoff for TM networks
  -M  Minimal predicted signal peptide length. Default: [10]
  -c  truncate to sequence length - 0 means no truncation. Default '70'
  -l  Logfile if -v is defined. Default: 'STDERR'
  -v  Verbose. Default: 'Off'
  -V  Print SignalP version and exit
  -h  Print this help information
</pre>
[[#top|Back to Top]]
=== Installation ===
source code from [http://www.cbs.dtu.dk/services/SignalP SignalP]
=== System ===
64-bit Linux

Latest revision as of 09:14, 5 June 2018

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