ClustalO settings

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4467 e3abac25-378b-4346-85de-24260fe3988d

diff --git a/conf/Engine.cluster.properties b/conf/Engine.cluster.properties
index caa2541..3c104f2 100644 (file)
--- a/conf/Engine.cluster.properties
+++ b/conf/Engine.cluster.properties
@@ -2,7 +2,7 @@
 \r
 # enable or disable engine true | false\r
 # OPTIONAL defaults to false\r
-engine.cluster.enable=false\r
+engine.cluster.enable=true\r
 \r
 # Directory to use for temporary files storage\r
 # REQUIRED - cluster nodes must have access to this directory!\r
@@ -12,7 +12,8 @@ engine.cluster.enable=false
 # to the job folders if this path is within JABA web application. \r
 # JABAWS statistic application just assume that the last name in the path is the \r
 # application folder in the root of JABAWS web application. \r
-cluster.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/jobsout\r
+#cluster.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/jobsout\r
+cluster.tmp.directory=/homes/pvtroshin/workspace/jaba2/jobsout\r
 \r
 # Enable/disable cluster statistics collector \r
 cluster.stat.collector.enable=false\r

diff --git a/conf/Executable.properties b/conf/Executable.properties
index 7471956..7864ebf 100644 (file)
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -74,13 +74,17 @@ clustalw.parameters.file=conf/settings/ClustalParameters.xml
 \r
 ######                 CLUSTAL OMEGA CONFIGURATION                ######\r
 local.clustalo.bin.windows=binaries/windows/clustalo/clustalo.exe\r
-local.clustalo.bin=binaries/src/clustalo/clustalo\r
-#cluster.clustalo.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalo/clustalo\r
+local.clustalo.bin=binaries/src/clustalo/src/clustalo\r
+cluster.clustalo.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalo/src/clustalo\r
 ## This parameters specifies the directory where the matrices files are stored   \r
-clustalo.presets.file=conf/settings/ClustalPresets.xml\r
-clustalo.parameters.file=conf/settings/ClustalParameters.xml\r
-#clustalo.limits.file=conf/settings/ClustalLimits.xml\r
-#clustalo.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+#clustalo.presets.file=conf/settings/ClustaloPresets.xml\r
+clustalo.parameters.file=conf/settings/ClustaloParameters.xml\r
+clustalo.limits.file=conf/settings/ClustaloLimits.xml\r
+## ClustalO can be executed on multiple CPUs if run on the cluster. \r
+## This parameter specifies the number of CPUs to use\r
+clustalo.cluster.cpunum=4\r
+## This reserves a slot with CPUNUM on the cluster for the task\r
+clustalo.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00  \r
 \r
 \r
 ######                 MUSCLE CONFIGURATION                 ######\r

diff --git a/conf/settings/ClustaloLimits.xml b/conf/settings/ClustaloLimits.xml
index ecb8148..1367ff3 100644 (file)
--- a/conf/settings/ClustaloLimits.xml
+++ b/conf/settings/ClustaloLimits.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
 <limits>\r
- <runnerClassName>compbio.runner.clustal.ClustalW</runnerClassName>\r
+ <runnerClassName>compbio.runner.clustal.ClustalO</runnerClassName>\r
        <limit isDefault="true">\r
-               <seqNumber>1000</seqNumber>\r
+               <seqNumber>2000</seqNumber>\r
                <seqLength>1000</seqLength>\r
        </limit>\r
        <limit isDefault="false">\r
@@ -10,12 +10,4 @@
                <seqNumber>30</seqNumber>\r
                <seqLength>500</seqLength>\r
        </limit>\r
-\r
-       <!-- Limits for presets -->\r
-       <limit isDefault="false">\r
-               <preset>Disable gap weighting (Speed-oriented)</preset>\r
-               <seqNumber>1000</seqNumber>\r
-               <seqLength>3000</seqLength>\r
-       </limit>\r
-\r
 </limits>\r

diff --git a/conf/settings/ClustaloPresets.xml b/conf/settings/ClustaloPresets.xml
deleted file mode 100644 (file)
index 3115006..0000000
--- a/conf/settings/ClustaloPresets.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
-<presets>\r
- <runnerClassName>compbio.runner.clustal.ClustalW</runnerClassName>\r
-       <preset>\r
-               <name>Disable gap weighting (Speed-oriented)</name>\r
-               <description></description>\r
-               <optlist>\r
-                       <option>-NOPGAP</option>\r
-                       <option>-NOWEIGHTS</option>\r
-                       <option>-NOHGAP</option>\r
-               </optlist>\r
-       </preset>\r
-</presets>\r