Generalizing configuration prior to release.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4336 e3abac25-378b-4346-85de-24260fe3988d

diff --git a/conf/Engine.cluster.properties b/conf/Engine.cluster.properties
index 344858b..caa2541 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=true\r
+engine.cluster.enable=false\r
 \r
 # Directory to use for temporary files storage\r
 # REQUIRED - cluster nodes must have access to this directory!\r
@@ -12,8 +12,7 @@ engine.cluster.enable=true
 # 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=/homes/pvtroshin/workspace/jaba2/jobsout \r
+cluster.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/jobsout\r
 \r
 # Enable/disable cluster statistics collector \r
 cluster.stat.collector.enable=false\r

diff --git a/conf/Engine.local.properties b/conf/Engine.local.properties
index 25fd766..2f211e8 100644 (file)
--- a/conf/Engine.local.properties
+++ b/conf/Engine.local.properties
@@ -5,7 +5,8 @@ engine.local.enable=true
 # Directory to use for temporary files storage\r
 # OPTIONAL defaults to java temporary directory \r
 # Relative path within the project will be converted in absolute at runtime\r
-local.tmp.directory=local_jobsout \r
+# /cluster/gjb_lab/fc/www-jws2/jaba/local_jobsout \r
+local.tmp.directory=jobsout \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
@@ -14,8 +15,8 @@ local.tmp.directory=local_jobsout
 #engine.local.thread.number=3\r
 \r
 # Enable/disable cluster statistics collector\r
-local.stat.collector.enable=false\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
+local.stat.maxruntime=24
\ No newline at end of file

diff --git a/conf/Executable.properties b/conf/Executable.properties
index caf7355..d43ff97 100644 (file)
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -1,3 +1,21 @@
+################################################################################\r
+# THIS IS JABAWS EXECUTABLE CONFIGURATION FILE                                 # \r
+################################################################################\r
+\r
+#File structure: \r
+\r
+# Uncomment this if you want to limit the size of the job to be accepted by a WS\r
+#clustalw.limits.file=conf/settings/ClustalLimits.xml\r
+\r
+# Uncomment this if you want to limit the size of the job to be accepted by a WS\r
+\r
+# Uncomment this if your what set a maximum execution time for this webservice \r
+# to 24 hours and maximum amount of memory per task to 6Gb. Please note that  \r
+# you may need to change this if your cluster scheduler is not SGE or OGE.  \r
+#mafft.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+\r
+# The number of CPU to use on the cluster by a Tcoffee \r
+#tcoffee.cluster.cpunum=4\r
 \r
 ### Clustal configuration ###\r
 local.clustalw.bin.windows=binaries/windows/clustalw2.exe\r
@@ -9,25 +27,22 @@ cluster.clustalw.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalw/src/
 clustalw.-matrix.path=binaries/matrices\r
 clustalw.presets.file=conf/settings/ClustalPresets.xml\r
 clustalw.parameters.file=conf/settings/ClustalParameters.xml\r
-clustalw.limits.file=conf/settings/ClustalLimits.xml\r
-clustalw.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+#clustalw.limits.file=conf/settings/ClustalLimits.xml\r
+#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/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/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
 muscle.presets.file=conf/settings/MusclePresets.xml\r
 muscle.parameters.file=conf/settings/MuscleParameters.xml\r
-muscle.limits.file=conf/settings/MuscleLimits.xml\r
-muscle.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+#muscle.limits.file=conf/settings/MuscleLimits.xml\r
+#muscle.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
 \r
 ### Mafft configuration ###\r
-#local.mafft.bin.windows=\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
@@ -35,62 +50,52 @@ mafft.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/
 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
+#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/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
-tcoffee.cluster.cpunum=4\r
-tcoffee.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00  \r
+#tcoffee.limits.file=conf/settings/TcoffeeLimits.xml\r
+#tcoffee.cluster.cpunum=4\r
+#tcoffee.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00  \r
 \r
 ### Probcons configuration ###\r
-#local.probcons.bin.windows=\r
 local.probcons.bin=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
+#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
+#jronn.parameters.file=conf/settings/JronnParameters.xml\r
+#jronn.limits.file=conf/settings/JronnLimits.xml\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
+#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
+#globplot.bin.env=PYTHONPATH#/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/biopython-1.50 \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
@@ -101,8 +106,8 @@ local.iupred.bin=binaries/src/iupred/iupred
 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
+#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
@@ -113,6 +118,5 @@ cluster.aacon.bin=/sw/java/latest/bin/java
 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
+#aacon.limits.file=conf/settings/AAConLimits.xml\r
+#aacon.cluster.cpunum=4\r

diff --git a/conf/settings/AAConLimits.xml b/conf/settings/AAConLimits.xml
index 5b066d9..5f9a482 100644 (file)
--- a/conf/settings/AAConLimits.xml
+++ b/conf/settings/AAConLimits.xml
@@ -10,6 +10,8 @@
                <seqNumber>200</seqNumber>\r
                <seqLength>400</seqLength>\r
        </limit>\r
+\r
+       <!-- Limits for presets -->\r
        <limit isDefault="false">\r
                <preset>Quick conservation</preset>\r
                <seqNumber>10000</seqNumber>\r
@@ -25,4 +27,5 @@
                <seqNumber>2000</seqNumber>\r
                <seqLength>1000</seqLength>\r
        </limit>\r
+\r
 </limits>\r

diff --git a/conf/settings/ClustalLimits.xml b/conf/settings/ClustalLimits.xml
index 52b0ef3..ecb8148 100644 (file)
--- a/conf/settings/ClustalLimits.xml
+++ b/conf/settings/ClustalLimits.xml
@@ -2,21 +2,20 @@
 <limits>\r
  <runnerClassName>compbio.runner.clustal.ClustalW</runnerClassName>\r
        <limit isDefault="true">\r
-               <seqNumber>100000</seqNumber>\r
-               <seqLength>100000</seqLength>\r
+               <seqNumber>1000</seqNumber>\r
+               <seqLength>1000</seqLength>\r
        </limit>\r
        <limit isDefault="false">\r
                <preset># LocalEngineExecutionLimit #</preset>\r
-               <seqNumber>100000</seqNumber>\r
-               <seqLength>100000</seqLength>\r
+               <seqNumber>30</seqNumber>\r
+               <seqLength>500</seqLength>\r
        </limit>\r
 \r
-       <!-- Uncomment/edit these if you would like to have separate limits for presets -->\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
+\r
 </limits>\r

diff --git a/conf/settings/MafftLimits.xml b/conf/settings/MafftLimits.xml
index 7067ff5..b3b3f81 100644 (file)
--- a/conf/settings/MafftLimits.xml
+++ b/conf/settings/MafftLimits.xml
@@ -2,17 +2,17 @@
 <limits>\r
  <runnerClassName>compbio.runner.mafft.Mafft</runnerClassName>\r
        <limit isDefault="true">\r
-               <seqNumber>100000</seqNumber>\r
-               <seqLength>100000</seqLength>\r
+               <seqNumber>1000</seqNumber>\r
+               <seqLength>1000</seqLength>\r
        </limit>\r
        <limit isDefault="false">\r
                <preset># LocalEngineExecutionLimit #</preset>\r
-               <seqNumber>100000</seqNumber>\r
-               <seqLength>100000</seqLength>\r
+               <seqNumber>20</seqNumber>\r
+               <seqLength>500</seqLength>\r
        </limit>\r
        \r
-       <!-- Uncomment/edit these if you would like to have separate limits for presets --> \r
-       <!-- \r
+       <!-- Limits for presets --> \r
+\r
        <limit isDefault="false">\r
                <preset>L-INS-i (Accuracy-oriented)</preset>\r
                <seqNumber>500</seqNumber>\r
@@ -43,6 +43,5 @@
                <seqNumber>2000</seqNumber>\r
                <seqLength>1000</seqLength>\r
        </limit>\r
-        -->\r
        \r
 </limits>\r

diff --git a/conf/settings/MuscleLimits.xml b/conf/settings/MuscleLimits.xml
index 2aceb46..b08f536 100644 (file)
--- a/conf/settings/MuscleLimits.xml
+++ b/conf/settings/MuscleLimits.xml
@@ -2,17 +2,16 @@
 <limits>\r
  <runnerClassName>compbio.runner.muscle.Muscle</runnerClassName>\r
        <limit isDefault="true">\r
-               <seqNumber>100000</seqNumber>\r
-               <seqLength>100000</seqLength>\r
+               <seqNumber>1000</seqNumber>\r
+               <seqLength>1000</seqLength>\r
        </limit>\r
        <limit isDefault="false">\r
                <preset># LocalEngineExecutionLimit #</preset>\r
-               <seqNumber>100000</seqNumber>\r
-               <seqLength>100000</seqLength>\r
+               <seqNumber>20</seqNumber>\r
+               <seqLength>500</seqLength>\r
        </limit>\r
        \r
-       <!-- Uncomment/edit these if you would like to have separate limits for presets -->\r
-       <!-- \r
+       <!-- Separate limits for presets        -->\r
        <limit isDefault="false">\r
                <preset>Protein alignment(Fastest speed)</preset>\r
                <seqNumber>2000</seqNumber>\r
@@ -28,6 +27,5 @@
                <seqNumber>2000</seqNumber>\r
                <seqLength>3000</seqLength>\r
        </limit>\r
-        -->\r
         \r
 </limits>\r

diff --git a/conf/settings/ProbconsLimits.xml b/conf/settings/ProbconsLimits.xml
index 1d871d7..e530fb9 100644 (file)
--- a/conf/settings/ProbconsLimits.xml
+++ b/conf/settings/ProbconsLimits.xml
@@ -2,12 +2,12 @@
 <limits>\r
  <runnerClassName>compbio.runner.probcons.Probcons</runnerClassName>\r
        <limit isDefault="true">\r
-               <seqNumber>100000</seqNumber>\r
-               <seqLength>100000</seqLength>\r
+               <seqNumber>1000</seqNumber>\r
+               <seqLength>1000</seqLength>\r
        </limit>\r
        <limit isDefault="false">\r
                <preset># LocalEngineExecutionLimit #</preset>\r
-               <seqNumber>100000</seqNumber>\r
-               <seqLength>100000</seqLength>\r
+               <seqNumber>20</seqNumber>\r
+               <seqLength>500</seqLength>\r
        </limit>\r
 </limits>\r

diff --git a/conf/settings/TcoffeeLimits.xml b/conf/settings/TcoffeeLimits.xml
index 660d27c..7e9dc9e 100644 (file)
--- a/conf/settings/TcoffeeLimits.xml
+++ b/conf/settings/TcoffeeLimits.xml
@@ -2,21 +2,20 @@
 <limits>\r
  <runnerClassName>compbio.runner.tcoffee.Tcoffee</runnerClassName>\r
        <limit isDefault="true">\r
-               <seqNumber>100000</seqNumber>\r
-               <seqLength>100000</seqLength>\r
+               <seqNumber>1000</seqNumber>\r
+               <seqLength>1000</seqLength>\r
        </limit>\r
        <limit isDefault="false">\r
                <preset># LocalEngineExecutionLimit #</preset>\r
-               <seqNumber>100000</seqNumber>\r
-               <seqLength>100000</seqLength>\r
+               <seqNumber>15</seqNumber>\r
+               <seqLength>400</seqLength>\r
        </limit>\r
-       \r
-       <!-- Uncomment/edit these if you would like to have separate limits for presets -->\r
-       <!-- \r
+\r
+       <!-- Limits for presets -->\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
-        -->\r
+\r
 </limits>\r