From ff4eb72e1d1a381dc9317c80fcc1b92fc1c68d17 Mon Sep 17 00:00:00 2001
From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Thu, 4 Aug 2011 13:19:45 +0000
Subject: [PATCH] ClustalO settings

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4467 e3abac25-378b-4346-85de-24260fe3988d
---
 conf/Engine.cluster.properties    |    5 +++--
 conf/Executable.properties        |   16 ++++++++++------
 conf/settings/ClustaloLimits.xml  |   12 ++----------
 conf/settings/ClustaloPresets.xml |   13 -------------
 4 files changed, 15 insertions(+), 31 deletions(-)
 delete mode 100644 conf/settings/ClustaloPresets.xml

diff --git a/conf/Engine.cluster.properties b/conf/Engine.cluster.properties
index caa2541..3c104f2 100644
--- a/conf/Engine.cluster.properties
+++ b/conf/Engine.cluster.properties
@@ -2,7 +2,7 @@
 
 # enable or disable engine true | false
 # OPTIONAL defaults to false
-engine.cluster.enable=false
+engine.cluster.enable=true
 
 # Directory to use for temporary files storage
 # REQUIRED - cluster nodes must have access to this directory!
@@ -12,7 +12,8 @@ engine.cluster.enable=false
 # to the job folders if this path is within JABA web application. 
 # JABAWS statistic application just assume that the last name in the path is the 
 # application folder in the root of JABAWS web application. 
-cluster.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/jobsout
+#cluster.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/jobsout
+cluster.tmp.directory=/homes/pvtroshin/workspace/jaba2/jobsout
 
 # Enable/disable cluster statistics collector 
 cluster.stat.collector.enable=false
diff --git a/conf/Executable.properties b/conf/Executable.properties
index 7471956..7864ebf 100644
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -74,13 +74,17 @@ clustalw.parameters.file=conf/settings/ClustalParameters.xml
 
 ######                 CLUSTAL OMEGA CONFIGURATION                ######
 local.clustalo.bin.windows=binaries/windows/clustalo/clustalo.exe
-local.clustalo.bin=binaries/src/clustalo/clustalo
-#cluster.clustalo.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalo/clustalo
+local.clustalo.bin=binaries/src/clustalo/src/clustalo
+cluster.clustalo.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalo/src/clustalo
 ## This parameters specifies the directory where the matrices files are stored   
-clustalo.presets.file=conf/settings/ClustalPresets.xml
-clustalo.parameters.file=conf/settings/ClustalParameters.xml
-#clustalo.limits.file=conf/settings/ClustalLimits.xml
-#clustalo.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
+#clustalo.presets.file=conf/settings/ClustaloPresets.xml
+clustalo.parameters.file=conf/settings/ClustaloParameters.xml
+clustalo.limits.file=conf/settings/ClustaloLimits.xml
+## ClustalO can be executed on multiple CPUs if run on the cluster. 
+## This parameter specifies the number of CPUs to use
+clustalo.cluster.cpunum=4
+## This reserves a slot with CPUNUM on the cluster for the task
+clustalo.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00  
 
 
 ######                 MUSCLE CONFIGURATION                 ######
diff --git a/conf/settings/ClustaloLimits.xml b/conf/settings/ClustaloLimits.xml
index ecb8148..1367ff3 100644
--- a/conf/settings/ClustaloLimits.xml
+++ b/conf/settings/ClustaloLimits.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
 <limits>
- <runnerClassName>compbio.runner.clustal.ClustalW</runnerClassName>
+ <runnerClassName>compbio.runner.clustal.ClustalO</runnerClassName>
 	<limit isDefault="true">
-		<seqNumber>1000</seqNumber>
+		<seqNumber>2000</seqNumber>
 		<seqLength>1000</seqLength>
 	</limit>
 	<limit isDefault="false">
@@ -10,12 +10,4 @@
 		<seqNumber>30</seqNumber>
 		<seqLength>500</seqLength>
 	</limit>
-
-	<!-- Limits for presets	-->
-	<limit isDefault="false">
-		<preset>Disable gap weighting (Speed-oriented)</preset>
-		<seqNumber>1000</seqNumber>
-		<seqLength>3000</seqLength>
-	</limit>
-
 </limits>
diff --git a/conf/settings/ClustaloPresets.xml b/conf/settings/ClustaloPresets.xml
deleted file mode 100644
index 3115006..0000000
--- a/conf/settings/ClustaloPresets.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
-<presets>
- <runnerClassName>compbio.runner.clustal.ClustalW</runnerClassName>
-	<preset>
-		<name>Disable gap weighting (Speed-oriented)</name>
-		<description></description>
-		<optlist>
-			<option>-NOPGAP</option>
-			<option>-NOWEIGHTS</option>
-			<option>-NOHGAP</option>
-		</optlist>
-	</preset>
-</presets>
-- 
1.7.10.2