JWS-67 configuration and manual file for jpred 3.0.1

diff --git a/conf/settings/JpredLimits.xml b/conf/settings/JpredLimits.xml
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+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
+<limits>\r
+    <runnerClassName>compbio.runner.predictors.Jpred</runnerClassName>\r
+    <limit isDefault="true">\r
+        <seqNumber>2000</seqNumber>\r
+        <seqLength>1000</seqLength>\r
+    </limit>\r
+    <limit isDefault="false">\r
+        <preset># LocalEngineExecutionLimit #</preset>\r
+        <seqNumber>30</seqNumber>\r
+        <seqLength>500</seqLength>\r
+    </limit>\r
+</limits>\r

diff --git a/conf/settings/JpredParameters.xml b/conf/settings/JpredParameters.xml
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+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
+<runnerConfig>\r
+    <runnerClassName>compbio.runner.predictors.Jpred</runnerClassName>\r
+\r
+    <options>\r
+        <name>Prediction without PSI-BLAST hits</name>\r
+        <description>\r
+            Toggle allowing Jpred to make predictions even when there are no\r
+            PSI-BLAST hits.\r
+        </description>\r
+        <optionNames>-pred-nohits</optionNames>\r
+        <furtherDetails>prog_docs/jpred.txt</furtherDetails>\r
+    </options>\r
+\r
+    <prmSeparator> </prmSeparator>\r
+\r
+    <parameters isRequired="false">\r
+        <name>UNIREF database</name>\r
+        <description>\r
+            Path to UNIREF database for PSI-BLAST querying\r
+        </description>\r
+        <optionNames>-dbpath</optionNames>\r
+        <furtherDetails>prog_docs/jpred.txt</furtherDetails>\r
+        <defaultValue>.</defaultValue>\r
+     </parameters>\r
+\r
+    <parameters isRequired="true">\r
+        <name>UNIREF database name</name>\r
+        <description>\r
+            Number of (combined guide tree/HMM) iterations\r
+        </description>\r
+        <optionNames>-dbname</optionNames>\r
+        <furtherDetails>prog_docs/jpred.txt</furtherDetails>\r
+        <defaultValue>ported_db</defaultValue>\r
+        <possibleValues>uniref90</possibleValues>\r
+        <possibleValues>ported_db</possibleValues>\r
+        <possibleValues>cluster</possibleValues>\r
+<!--\r
+experimental development databases:\r
+        <possibleValues>training</possibleValues>\r
+        <possibleValues>swall</possibleValues>\r
+        <possibleValues>uniprot</possibleValues>\r
+        <possibleValues>uniref50</possibleValues>\r
+-->\r
+    </parameters>\r
+\r
+     <parameters isRequired="false">\r
+        <name>Number of CPUs</name>\r
+        <description>\r
+            Number of CPU used by jpred.pl. Maximum value is 8\r
+        </description>\r
+        <optionNames>-ncpu</optionNames>\r
+        <furtherDetails>prog_docs/jpred.txt</furtherDetails>\r
+        <defaultValue>1</defaultValue>\r
+        <validValue>\r
+            <type>Integer</type>\r
+            <min>1</min>\r
+            <max>8</max>\r
+        </validValue>\r
+    </parameters>\r
+\r
+    <parameters isRequired="false">\r
+        <name>PSI-BLAST output file</name>\r
+        <description>\r
+            Path to a PSI-BLAST output file\r
+        </description>\r
+        <optionNames>-psi</optionNames>\r
+        <furtherDetails>prog_docs/jpred.txt</furtherDetails>\r
+        <defaultValue></defaultValue>\r
+    </parameters>\r
+</runnerConfig>\r

diff --git a/conf/settings/JpredPresets.xml b/conf/settings/JpredPresets.xml
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+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
+<presets>\r
+    <runnerClassName>compbio.runner.predictors.Jpred</runnerClassName>\r
+\r
+    <preset>\r
+        <name>cluser configuration</name>\r
+        <description>\r
+            Dundee cluser configuration\r
+        </description>\r
+        <optlist>\r
+            <option>-dbpath /homes/www-jpred/databases </option>\r
+            <option>-dbname uniref90</option>\r
+        </optlist>\r
+    </preset>\r
+\r
+    <preset>\r
+        <name>laptop configuration</name>\r
+        <description>\r
+            My 4-core laptop configuration\r
+        </description>\r
+        <optlist>\r
+            <option>-dbpath /data/UNIREFdb</option>\r
+            <option>-dbname ported_db</option>\r
+            <option>-ncpu 4</option>\r
+        </optlist>\r
+    </preset>\r
+\r
+</presets>\r

diff --git a/website/prog_docs/jpred.txt b/website/prog_docs/jpred.txt
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+Usage:
+    ./jpred.pl -in/-sequence <FILE1> [-out/-output <FILEPREFIX>] [-dbname
+    <DBNAME>] [-dbpath <PATH>] [-ncpu NNN] [-psi <psiblast output>]
+    [-pred-nohits] [-verbose] [-debug] [-help] [-man]
+
+Options:
+    -in/-sequence FILE
+         The path to the sequence file (in FASTA format) you want to
+         predict.
+
+    -out/-output FILEPREFIX
+         A prefix to the filenames created by Jpred, defaults to the value
+         set by -sequence/-in.
+
+    -dbpath PATH
+         Path to the uniref database used for PSI-BLAST querying.
+         Default: .
+
+    -dbname database
+         Database to use for PSI-BLAST querying. This only accepts databases
+         from a list which is pre-defined in the code.
+         Default: uniref90
+
+    -psi path
+         Path to a PSI-BLAST output file.
+
+    -ncpu NNN
+         Number of CPU used by jpred.pl. Maximum value is 8
+         Default: NNN = 1
+
+    -pred-nohits
+         Toggle allowing Jpred to make predictions even when there are no
+         PSI-BLAST hits.
+
+    -verbose
+         Verbose mode. Print more information while running jpred.
+
+    -debug
+         Debug mode. Print debugging information while running jpred.
+
+    -help
+         Gives help on the programs usage.
+
+    -man Displays this man page.
+