From d58f92e0f06498d2f18d9b40c932989cb038f3de Mon Sep 17 00:00:00 2001
From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Fri, 2 Aug 2013 11:32:09 +0100
Subject: [PATCH] JWS-67 configuration and manual file for jpred 3.0.1

---
 conf/settings/JpredLimits.xml     |   13 +++++++
 conf/settings/JpredParameters.xml |   71 +++++++++++++++++++++++++++++++++++++
 conf/settings/JpredPresets.xml    |   28 +++++++++++++++
 website/prog_docs/jpred.txt       |   45 +++++++++++++++++++++++
 4 files changed, 157 insertions(+)
 create mode 100644 conf/settings/JpredLimits.xml
 create mode 100644 conf/settings/JpredParameters.xml
 create mode 100644 conf/settings/JpredPresets.xml
 create mode 100644 website/prog_docs/jpred.txt

diff --git a/conf/settings/JpredLimits.xml b/conf/settings/JpredLimits.xml
new file mode 100644
index 0000000..3180ec5
--- /dev/null
+++ b/conf/settings/JpredLimits.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
+<limits>
+    <runnerClassName>compbio.runner.predictors.Jpred</runnerClassName>
+    <limit isDefault="true">
+        <seqNumber>2000</seqNumber>
+        <seqLength>1000</seqLength>
+    </limit>
+    <limit isDefault="false">
+        <preset># LocalEngineExecutionLimit #</preset>
+        <seqNumber>30</seqNumber>
+        <seqLength>500</seqLength>
+    </limit>
+</limits>
diff --git a/conf/settings/JpredParameters.xml b/conf/settings/JpredParameters.xml
new file mode 100644
index 0000000..03c6906
--- /dev/null
+++ b/conf/settings/JpredParameters.xml
@@ -0,0 +1,71 @@
+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
+<runnerConfig>
+    <runnerClassName>compbio.runner.predictors.Jpred</runnerClassName>
+
+    <options>
+        <name>Prediction without PSI-BLAST hits</name>
+        <description>
+            Toggle allowing Jpred to make predictions even when there are no
+            PSI-BLAST hits.
+        </description>
+        <optionNames>-pred-nohits</optionNames>
+        <furtherDetails>prog_docs/jpred.txt</furtherDetails>
+    </options>
+
+    <prmSeparator> </prmSeparator>
+
+    <parameters isRequired="false">
+        <name>UNIREF database</name>
+        <description>
+            Path to UNIREF database for PSI-BLAST querying
+        </description>
+        <optionNames>-dbpath</optionNames>
+        <furtherDetails>prog_docs/jpred.txt</furtherDetails>
+        <defaultValue>.</defaultValue>
+     </parameters>
+
+    <parameters isRequired="true">
+        <name>UNIREF database name</name>
+        <description>
+            Number of (combined guide tree/HMM) iterations
+        </description>
+        <optionNames>-dbname</optionNames>
+        <furtherDetails>prog_docs/jpred.txt</furtherDetails>
+        <defaultValue>ported_db</defaultValue>
+        <possibleValues>uniref90</possibleValues>
+        <possibleValues>ported_db</possibleValues>
+        <possibleValues>cluster</possibleValues>
+<!--
+experimental development databases:
+        <possibleValues>training</possibleValues>
+        <possibleValues>swall</possibleValues>
+        <possibleValues>uniprot</possibleValues>
+        <possibleValues>uniref50</possibleValues>
+-->
+    </parameters>
+
+     <parameters isRequired="false">
+        <name>Number of CPUs</name>
+        <description>
+            Number of CPU used by jpred.pl. Maximum value is 8
+        </description>
+        <optionNames>-ncpu</optionNames>
+        <furtherDetails>prog_docs/jpred.txt</furtherDetails>
+        <defaultValue>1</defaultValue>
+        <validValue>
+            <type>Integer</type>
+            <min>1</min>
+            <max>8</max>
+        </validValue>
+    </parameters>
+
+    <parameters isRequired="false">
+        <name>PSI-BLAST output file</name>
+        <description>
+            Path to a PSI-BLAST output file
+        </description>
+        <optionNames>-psi</optionNames>
+        <furtherDetails>prog_docs/jpred.txt</furtherDetails>
+        <defaultValue></defaultValue>
+    </parameters>
+</runnerConfig>
diff --git a/conf/settings/JpredPresets.xml b/conf/settings/JpredPresets.xml
new file mode 100644
index 0000000..51f3d30
--- /dev/null
+++ b/conf/settings/JpredPresets.xml
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
+<presets>
+    <runnerClassName>compbio.runner.predictors.Jpred</runnerClassName>
+
+    <preset>
+        <name>cluser configuration</name>
+        <description>
+            Dundee cluser configuration
+        </description>
+        <optlist>
+            <option>-dbpath /homes/www-jpred/databases </option>
+            <option>-dbname uniref90</option>
+        </optlist>
+    </preset>
+
+    <preset>
+        <name>laptop configuration</name>
+        <description>
+            My 4-core laptop configuration
+        </description>
+        <optlist>
+            <option>-dbpath /data/UNIREFdb</option>
+            <option>-dbname ported_db</option>
+            <option>-ncpu 4</option>
+        </optlist>
+    </preset>
+
+</presets>
diff --git a/website/prog_docs/jpred.txt b/website/prog_docs/jpred.txt
new file mode 100644
index 0000000..7ef389f
--- /dev/null
+++ b/website/prog_docs/jpred.txt
@@ -0,0 +1,45 @@
+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.
+
-- 
1.7.10.2