remove settings as separate settings no longer required

Add separate conf setting for engines and executables for dundee

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4334 e3abac25-378b-4346-85de-24260fe3988d

diff --git a/dundee-conf/Engine.cluster.properties b/dundee-conf/Engine.cluster.properties
index 5264236..d75c228 100644 (file)
--- a/dundee-conf/Engine.cluster.properties
+++ b/dundee-conf/Engine.cluster.properties
@@ -7,5 +7,17 @@ engine.cluster.enable=true
 # Directory to use for temporary files storage\r
 # REQUIRED - cluster nodes must have access to this directory!\r
 # An absolute path is required \r
+\r
+# Please note that statistic web application will only be able to generate links\r
+# 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
+ \r
+\r
+# Enable/disable cluster statistics collector \r
+cluster.stat.collector.enable=true\r
 \r
+# Maximum amount of time the job is considered running in hours\r
+# Optional defaults to 7 days (168h) \r
+cluster.stat.maxruntime=24\r

diff --git a/dundee-conf/Engine.local.properties b/dundee-conf/Engine.local.properties
index a0c59d1..d9314c2 100644 (file)
--- a/dundee-conf/Engine.local.properties
+++ b/dundee-conf/Engine.local.properties
@@ -12,3 +12,10 @@ local.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/local_jobsout
 # OPTIONAL defaults to the number of cores for core number <=4 and \r
 # number of cores-1 for greater core numbers\r
 engine.local.thread.number=2\r
+\r
+# Enable/disable cluster statistics collector\r
+local.stat.collector.enable=true\r
+\r
+# Maximum amount of time the job is considered running in hours\r
+# Optional defaults to 24 hours\r
+local.stat.maxruntime=6
\ No newline at end of file

diff --git a/dundee-conf/Engine.local.sample.properties b/dundee-conf/Engine.local.sample.properties
deleted file mode 100644 (file)
index 1486480..0000000
--- a/dundee-conf/Engine.local.sample.properties
+++ /dev/null
@@ -1,15 +0,0 @@
-### Local Binaries root path ###\r
-# enable or disable engine true | false\r
-# OPTIONAL defaults to true\r
-engine.local.enable=true \r
-\r
-# Directory to use for temporary files storage\r
-# OPTIONAL defaults to java temporary directory \r
-local.tmp.directory=D:\\workspace\\clusterengine\\testoutput \r
- \r
-# Number of threads for tasks execution (valid values between 1 and 2x cpu. \r
-# Where x is a number of cores available in the system)\r
-# OPTIONAL defaults to the number of cores for core number <=4 and \r
-# number of cores -1 for greater core numbers\r
-# TODO  \r
-engine.local.thread.number=\r

diff --git a/dundee-conf/Executable.properties b/dundee-conf/Executable.properties
index 3368475..caf7355 100644 (file)
--- a/dundee-conf/Executable.properties
+++ b/dundee-conf/Executable.properties
@@ -1,8 +1,8 @@
 \r
 ### Clustal configuration ###\r
-local.clustalw.bin.windows=binaries/clustalw2.exe\r
+local.clustalw.bin.windows=binaries/windows/clustalw2.exe\r
 local.clustalw.bin=binaries/src/clustalw/src/clustalw2\r
-cluster.clustalw.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/clustalw/src/clustalw2\r
+cluster.clustalw.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalw/src/clustalw2\r
 # Parameters names which come from RunnerConfig -> Parameters.xml file ultimately are all lowercased in comparison!\r
 # see engine.client.Util.getExecProperty() method for details  \r
 # So they are case insensitive. \r
@@ -13,11 +13,11 @@ clustalw.limits.file=conf/settings/ClustalLimits.xml
 clustalw.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
 \r
 ### Muscle configuration ###\r
-local.muscle.bin.windows=binaries/muscle.exe\r
+local.muscle.bin.windows=binaries/windows/muscle.exe\r
 local.muscle.bin=binaries/src/muscle/muscle\r
 # Beware version of muscle on the cluster older and does not support some \r
 # of the newer version attributed thus, will not work with Muscle.java wrapper!\r
-cluster.muscle.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/muscle/muscle\r
+cluster.muscle.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/muscle/muscle\r
 #The environment variable MUSCLE_MXPATH can be used to specify a path where the matrices are stored\r
 # e.g. MUSCLE_MXPATH#binaries/matrices - but need to privide absolute path!\r
 muscle.-matrix.path=binaries/matrices\r
@@ -28,21 +28,25 @@ muscle.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
 \r
 ### Mafft configuration ###\r
 #local.mafft.bin.windows=\r
-local.mafft.bin=binaries/src/mafft/binaries/mafft\r
-cluster.mafft.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/mafft/binaries/mafft\r
-mafft.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#/sw/bin/fasta34;\r
+local.mafft.bin=binaries/src/mafft/scripts/mafft\r
+cluster.mafft.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/mafft/scripts/mafft\r
+# These paths will be converted to absolute if relative.\r
+mafft.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;\r
 mafft.--aamatrix.path=binaries/matrices\r
 mafft.presets.file=conf/settings/MafftPresets.xml\r
 mafft.parameters.file=conf/settings/MafftParameters.xml\r
 mafft.limits.file=conf/settings/MafftLimits.xml\r
 mafft.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
 \r
+\r
 ### Tcoffee configuration ###\r
 local.tcoffee.bin=binaries/src/tcoffee/t_coffee_source/t_coffee\r
-cluster.tcoffee.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/tcoffee/t_coffee_source/t_coffee\r
+cluster.tcoffee.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/tcoffee/t_coffee_source/t_coffee\r
 #/sw/bin/t_coffee\r
 # Sub matrix support does not work \r
 #tcoffee.-matrix.path=binaries/matrices\r
+# This variable is required by tcoffee\r
+tcoffee.bin.env=HOME_4_TCOFFEE#jobsout;\r
 tcoffee.presets.file=conf/settings/TcoffeePresets.xml\r
 tcoffee.parameters.file=conf/settings/TcoffeeParameters.xml\r
 tcoffee.limits.file=conf/settings/TcoffeeLimits.xml\r
@@ -52,8 +56,63 @@ tcoffee.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -
 ### Probcons configuration ###\r
 #local.probcons.bin.windows=\r
 local.probcons.bin=binaries/src/probcons/probcons\r
-cluster.probcons.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/probcons/probcons\r
+cluster.probcons.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/probcons/probcons\r
 #Probcons does not support matrix loading - unrecognised option reported! \r
 probcons.parameters.file=conf/settings/ProbconsParameters.xml\r
 probcons.limits.file=conf/settings/ProbconsLimits.xml\r
 probcons.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+\r
+### Jronn configuration ### \r
+local.jronn.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe \r
+local.jronn.bin=/sw/java/latest/bin/java\r
+cluster.jronn.bin=/sw/java/latest/bin/java\r
+jronn.jar.file=binaries/windows/jronn3.1.jar\r
+# jronn.parameters.file=conf/settings/JronnParameters.xml\r
+jronn.limits.file=conf/settings/JronnLimits.xml\r
+#TODO jronn.jvm.options=-Xms32M -Xmx512M\r
+jronn.cluster.cpunum=4\r
+jronn.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
+### Disembl configuration Tisean - Disembl dependancy ### \r
+#local.disembl.bin.windows= \r
+local.disembl.bin=binaries/src/disembl/DisEMBL.py\r
+cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py\r
+# disembl.parameters.file=conf/settings/DisemblParameters.xml\r
+disembl.limits.file=conf/settings/DisemblLimits.xml\r
+disembl.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+\r
+### GlobPlot configuration Tisean - GlobPlot and Disembl dependancy ### \r
+#local.disembl.bin.windows= \r
+local.globplot.bin=binaries/src/globplot/GlobPlot.py\r
+cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/GlobPlot.py\r
+# Dundee only settings\r
+globplot.bin.env=PYTHONPATH#/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/biopython-1.50 \r
+# globplot.parameters.file=conf/settings/GlobPlotParameters.xml\r
+globplot.limits.file=conf/settings/GlobPlotLimits.xml\r
+globplot.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+\r
+### IUPred configuration ### \r
+local.iupred.bin.windows=binaries/windows/iupred/iupred.exe \r
+local.iupred.bin=binaries/src/iupred/iupred\r
+# This must point to the directory where iupred binary is, with other files it depends on\r
+#iupred.bin.env=IUPred_PATH#/homes/pvtroshin/workspace/jaba2/binaries/src/iupred\r
+# This path will be converted to absolute if relative. \r
+iupred.bin.env=IUPred_PATH#binaries/src/iupred\r
+cluster.iupred.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/iupred/iupred\r
+iupred.parameters.file=conf/settings/IUPredParameters.xml\r
+iupred.limits.file=conf/settings/IUPredLimits.xml\r
+iupred.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+\r
+### AACon configuration ###\r
+# This is just a path to the standard java executable \r
+local.aacon.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe \r
+local.aacon.bin=/sw/java/latest/bin/java\r
+cluster.aacon.bin=/sw/java/latest/bin/java\r
+# Path to the AACon library\r
+aacon.jar.file=binaries/windows/aaconservation.jar\r
+aacon.parameters.file=conf/settings/AAConParameters.xml\r
+aacon.presets.file=conf/settings/AAConPresets.xml\r
+aacon.limits.file=conf/settings/AAConLimits.xml\r
+#TODO jronn.jvm.options=-Xms32M -Xmx512M\r
+aacon.cluster.cpunum=4\r

diff --git a/dundee-conf/settings/ClustalLimits.xml b/dundee-conf/settings/ClustalLimits.xml
deleted file mode 100644 (file)
index 28adf27..0000000
--- a/dundee-conf/settings/ClustalLimits.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
-<limits>\r
- <runnerClassName>compbio.runner.clustal.ClustalW</runnerClassName>\r
-       <limit isDefault="false">\r
-               <preset>Disable gap weighting (Speed-oriented)</preset>\r
-               <seqNumber>2000</seqNumber>\r
-               <seqLength>1000</seqLength>\r
-       </limit>\r
-       <limit isDefault="true">\r
-               <seqNumber>1000</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/dundee-conf/settings/MafftLimits.xml b/dundee-conf/settings/MafftLimits.xml
deleted file mode 100644 (file)
index 4cd787f..0000000
--- a/dundee-conf/settings/MafftLimits.xml
+++ /dev/null
@@ -1,43 +0,0 @@
-<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
-<limits>\r
- <runnerClassName>compbio.runner.mafft.Mafft</runnerClassName>\r
-       <limit isDefault="true">\r
-               <seqNumber>1000</seqNumber>\r
-               <seqLength>1000</seqLength>\r
-       </limit>\r
-       <limit isDefault="false">\r
-               <preset>L-INS-i (Accuracy-oriented)</preset>\r
-               <seqNumber>500</seqNumber>\r
-               <seqLength>1000</seqLength>\r
-       </limit>\r
-       <limit isDefault="false">\r
-               <preset>G-INS-i (Accuracy-oriented)</preset>\r
-               <seqNumber>500</seqNumber>\r
-               <seqLength>1000</seqLength>\r
-       </limit>\r
-       <limit isDefault="false">\r
-               <preset>E-INS-i (Accuracy-oriented)</preset>\r
-               <seqNumber>500</seqNumber>\r
-               <seqLength>1000</seqLength>\r
-       </limit>\r
-       <limit isDefault="false">\r
-               <preset>FFT-NS-i (Speed oriented)</preset>\r
-               <seqNumber>2000</seqNumber>\r
-               <seqLength>1000</seqLength>\r
-       </limit>\r
-       <limit isDefault="false">\r
-               <preset>FFT-NS-1 (Speed oriented)</preset>\r
-               <seqNumber>2000</seqNumber>\r
-               <seqLength>1000</seqLength>\r
-       </limit>\r
-       <limit isDefault="false">\r
-               <preset>NW-NS-PartTree-1 (Speed oriented)</preset>\r
-               <seqNumber>2000</seqNumber>\r
-               <seqLength>1000</seqLength>\r
-       </limit>\r
-       <limit isDefault="false">\r
-               <preset># LocalEngineExecutionLimit #</preset>\r
-               <seqNumber>20</seqNumber>\r
-               <seqLength>500</seqLength>\r
-       </limit>\r
-</limits>\r

diff --git a/dundee-conf/settings/MuscleLimits.xml b/dundee-conf/settings/MuscleLimits.xml
deleted file mode 100644 (file)
index 75d66d9..0000000
--- a/dundee-conf/settings/MuscleLimits.xml
+++ /dev/null
@@ -1,28 +0,0 @@
-<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
-<limits>\r
- <runnerClassName>compbio.runner.muscle.Muscle</runnerClassName>\r
-       <limit isDefault="true">\r
-               <seqNumber>1000</seqNumber>\r
-               <seqLength>1000</seqLength>\r
-       </limit>\r
-       <limit isDefault="false">\r
-               <preset>Protein alignment(Fastest speed)</preset>\r
-               <seqNumber>2000</seqNumber>\r
-               <seqLength>1000</seqLength>\r
-       </limit>\r
-       <limit isDefault="false">\r
-               <preset>Nucleotide alignment(Fastest speed)</preset>\r
-               <seqNumber>1000</seqNumber>\r
-               <seqLength>3000</seqLength>\r
-       </limit>\r
-       <limit isDefault="false">\r
-               <preset>Huge alignments (speed-oriented)</preset>\r
-               <seqNumber>2000</seqNumber>\r
-               <seqLength>3000</seqLength>\r
-       </limit>\r
-       <limit isDefault="false">\r
-               <preset># LocalEngineExecutionLimit #</preset>\r
-               <seqNumber>20</seqNumber>\r
-               <seqLength>500</seqLength>\r
-       </limit>\r
-</limits>\r

diff --git a/dundee-conf/settings/ProbconsLimits.xml b/dundee-conf/settings/ProbconsLimits.xml
deleted file mode 100644 (file)
index e530fb9..0000000
--- a/dundee-conf/settings/ProbconsLimits.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
-<limits>\r
- <runnerClassName>compbio.runner.probcons.Probcons</runnerClassName>\r
-       <limit isDefault="true">\r
-               <seqNumber>1000</seqNumber>\r
-               <seqLength>1000</seqLength>\r
-       </limit>\r
-       <limit isDefault="false">\r
-               <preset># LocalEngineExecutionLimit #</preset>\r
-               <seqNumber>20</seqNumber>\r
-               <seqLength>500</seqLength>\r
-       </limit>\r
-</limits>\r

diff --git a/dundee-conf/settings/TcoffeeLimits.xml b/dundee-conf/settings/TcoffeeLimits.xml
deleted file mode 100644 (file)
index 84b3f50..0000000
--- a/dundee-conf/settings/TcoffeeLimits.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
-<limits>\r
- <runnerClassName>compbio.runner.tcoffee.Tcoffee</runnerClassName>\r
-       <limit isDefault="true">\r
-               <seqNumber>1000</seqNumber>\r
-               <seqLength>1000</seqLength>\r
-       </limit>\r
-       <limit isDefault="false">\r
-               <preset>Quick align. Very fast approximate (Speed-oriented)</preset>\r
-               <seqNumber>1000</seqNumber>\r
-               <seqLength>3000</seqLength>\r
-       </limit>\r
-       <limit isDefault="false">\r
-               <preset># LocalEngineExecutionLimit #</preset>\r
-               <seqNumber>15</seqNumber>\r
-               <seqLength>400</seqLength>\r
-       </limit>\r
-</limits>\r
-\r