Pre release Executable.properties, help added, unused properties commented out

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4393 e3abac25-378b-4346-85de-24260fe3988d

diff --git a/conf/Executable.properties b/conf/Executable.properties
index 5bd5b6e..4ce8e13 100644 (file)
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -2,51 +2,94 @@
 # THIS IS JABAWS EXECUTABLE CONFIGURATION FILE                                 # \r
 ################################################################################\r
 \r
-#File structure: \r
+## Properties supported by all executables: \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
+## Path to the native executable on windows, \r
+## the path must be either absolute, or relative to JABAWS web application   \r
+# local.<execname>.bin.windows=binaries/windows/clustalw2.exe\r
 \r
-# Uncomment this if you want to limit the size of the job to be accepted by a WS\r
+## Path to the native executable not on windows (e.g. Linux, Mac)\r
+## the path must be either absolute, or relative to JABAWS web application\r
+# local.<execname>.bin=binaries/src/clustalw/src/clustalw2\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
+## Path to the native executable on the cluster (must be accessible from all \r
+## cluster nodes which will run JABAWS jobs). The path must be absolute. \r
+# cluster.<execname>.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalw/src/clustalw2\r
 \r
-# The number of CPU to use on the cluster by a Tcoffee \r
-#tcoffee.cluster.cpunum=4\r
+## At least one of the path to the native executable should be defined!\r
+ \r
+## Application supported presets, absolute or relative to \r
+## the JABAWS web application path to the file. Optional.\r
+# <execname>.presets.file=conf/settings/ClustalPresets.xml\r
+\r
+## Application supported parameters, absolute or relative to \r
+## the JABAWS web application path to the file. Optional. \r
+# <execname>.parameters.file=conf/settings/ClustalParameters.xml\r
+\r
+## Application limits, absolute or relative to \r
+## the JABAWS web application path to the file. Optional.\r
+## Use this if you want to limit the size of the job to be accepted by a \r
+## Webservice. The limits files we use in Dundee are provided with JABAWS. \r
+# <execname>.limits.file=conf/settings/ClustalLimits.xml\r
+\r
+## Flags passed to the cluster batch manager for the application. Optional.\r
+## This example sets a maximum execution time to 24 hours and maximum amount of \r
+## memory per task to 6Gb for SGE and OGE cluster batch managers.\r
+## Please note that all the examples of this parameter below are correct for \r
+## Sun Grid Engine or Open Grid Engine (untested) only! If you use a different \r
+## batch manager you would need to specify different flags.  \r
+# <execname>.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+\r
+## Environmental variables required by native executables. Optional. \r
+## Format: VARIABLE_NAME1#VARIABLE_VALUE1;VARIABLE_NAME2#VARIABLE_VALUE2; \r
+#<execname>.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;\r
+\r
+# Where <execname> is one of [clustalw, mafft, muscle, propcons, tcoffee,\r
+# iupred, jronn, globplot, disembl, aacon]\r
+\r
+\r
+####            Parameters specific to the JAVA Jar executables.        #### \r
 \r
-### Clustal configuration ###\r
+## Parameter supported by the executable Jar files, such as jronn and aacon, \r
+## point to the location of the jar file. Also, local.<execname>.bin, \r
+## local.<execname>.bin.windows properties are optional for these, if not \r
+## provided they will be replaced to the java executable path from JAVA_HOME \r
+## environmental variable. \r
+#<execname>.jar.file=binaries/windows/jronn3.1.jar\r
+\r
+  \r
+\r
+\r
+######                 CLUSTAL CONFIGURATION                ######\r
 local.clustalw.bin.windows=binaries/windows/clustalw2.exe\r
 local.clustalw.bin=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
+## This parameters specifies the directory where the matrices files are stored   \r
 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
 \r
-### Muscle configuration ###\r
+\r
+######                 MUSCLE CONFIGURATION                 ######\r
 local.muscle.bin.windows=binaries/windows/muscle.exe\r
 local.muscle.bin=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
+## This parameters specifies the directory where the matrices files are stored\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
 \r
-### Mafft configuration ###\r
+\r
+#####                  MAFFT CONFIGURATION                  ######\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
+## This parameters specifies the directory where the matrices files are stored\r
 mafft.--aamatrix.path=binaries/matrices\r
 mafft.presets.file=conf/settings/MafftPresets.xml\r
 mafft.parameters.file=conf/settings/MafftParameters.xml\r
@@ -54,7 +97,7 @@ mafft.parameters.file=conf/settings/MafftParameters.xml
 #mafft.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
 \r
 \r
-### Tcoffee configuration ###\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
 # This variable is required by tcoffee\r
@@ -62,55 +105,65 @@ tcoffee.bin.env=HOME_4_TCOFFEE#jobsout;
 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 can be executed on multiple CPUs if run on the cluster. \r
+## This parameter specifies the number of CPUs to use\r
 #tcoffee.cluster.cpunum=4\r
+## This reserves a slot with CPUNUM on the cluster for the task\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
+\r
+#####                  PROBCONS CONFIGURATION                ######\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
 \r
-### Jronn configuration ###\r
-# If no local path are specified, Java is loaded from JAVA_HOME environment \r
-# variable for local execution \r
+\r
+#####                  JRONN CONFIGURATION                   ######\r
+## If no local path is specified, Java is loaded from JAVA_HOME environment \r
+## variable for local execution. However, cluster.jronn.bin must be specified for \r
+## running Jronn on the cluster.  \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.limits.file=conf/settings/JronnLimits.xml\r
+#jronn.limits.file=conf/settings/JronnLimits.xml\r
+## Jronn can use multiple CPUs\r
+## This parameter specifies the number of CPU to use\r
 #jronn.cluster.cpunum=4\r
+## This reserves a slot with CPUNUM on the cluster for the task\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
+#####                  DISEMBL CONFIGURATION                 ###### \r
 local.disembl.bin=binaries/src/disembl/DisEMBL.py\r
 #cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py\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
+\r
+#####                  GLOBPLOT CONFIGURATION                ###### \r
 local.globplot.bin=binaries/src/globplot/GlobPlot.py\r
 #cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/GlobPlot.py\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
+\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
+## This must point to the directory where iupred binary is, with other files it \r
+## depends on. This path will be converted to absolute if relative at runtime. \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
+\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
@@ -120,5 +173,8 @@ aacon.jar.file=binaries/windows/aaconservation.jar
 aacon.parameters.file=conf/settings/AAConParameters.xml\r
 aacon.presets.file=conf/settings/AAConPresets.xml\r
 #aacon.limits.file=conf/settings/AAConLimits.xml\r
+## AACon can use multiple CPUs\r
+## This parameter specifies the number of CPUs to use\r
 #aacon.cluster.cpunum=4\r
+## This reserves a slot with CPUNUM on the cluster for the task\r
 #aacon.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00\r