JWS-67 Add Jpred to configuration files

diff --git a/build.xml b/build.xml
index e0ad3a4..4fbafe9 100644 (file)
--- a/build.xml
+++ b/build.xml
@@ -19,7 +19,7 @@
        <property name="compbio-ga" value="compbio-ga-1.0.jar"/>
 
        <!-- products -->
-       <property name="jabaws_version" value="3.0.0"/>
+       <property name="jabaws_version" value="2.5.0"/>
        <property name="datamodel" value="${distdir}/datamodel-${jabaws_version}.jar"/>
        <property name="datamodel-src" value="${distdir}/datamodel-src-${jabaws_version}.jar"/>
        <property name="min-jabaws-client" value="${distdir}/min-jabaws-client-${jabaws_version}.jar"/>
@@ -80,7 +80,7 @@
        <!-- Clean temp directories -->
        <target name="clean">
                <delete dir="${classes}" />
-               <delete dir="${basedir}/tmplog" />
+               <delete dir="${basedir}/logs" />
                <delete file="${distdir}/binaries.zip" />
                <delete file="${basedir}/activity.log" />
                <delete file="${basedir}/derby.log" />

diff --git a/conf/Executable.properties b/conf/Executable.properties
index 9e2ccb4..c3d6e52 100644 (file)
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -1,30 +1,36 @@
-################################################################################\r
-# THIS IS JABAWS EXECUTABLE CONFIGURATION FILE                                 # \r
-################################################################################\r
+###########################################################################################\r
+#                                                                                         #\r
+#            THIS IS JABAWS EXECUTABLE CONFIGURATION FILE                                 #\r
+#                                                                                         #\r
+###########################################################################################\r
 \r
-## Properties supported by all executables: \r
+### Properties supported by executables.\r
+### <execname> is one of the available applications: \r
+### [clustalw, mafft, muscle, propcons, tcoffee, iupred, jronn, globplot, disembl, aacon, jpred]\r
 \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
+### Path to the native executable on Windows must be either absolute, \r
+### or relative to JABAWS web application\r
+# local.<execname>.bin.windows = binaries/windows/clustalw2.exe\r
 \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
+### Path to the native executable not on Windows (e.g. Linux, Mac)\r
+### must be either absolute, or relative to JABAWS web application\r
+# local.<execname>.bin = binaries/src/clustalw/src/clustalw2\r
 \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
+### 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 = /home/jabaws/binaries/src/clustalw/src/clustalw2\r
 \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
+### At least one of the path to the native executable should be defined.\r
+\r
+### If an application supports presets, the preset file can have either  \r
+### absolute or relative to the JABAWS web application path to the file. \r
+### The file is 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
+### If an application supports parameters, the parameter file can have either \r
+### absolute or relative to the JABAWS web application path to the file. \r
+### The file is 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
@@ -38,159 +44,183 @@
 ## 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
+# <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
+# <execname>.bin.env = MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;\r
 \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/bj3.0.4p-jronn.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
-## 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 ram=6000M\r
-\r
-\r
-######                 CLUSTAL OMEGA CONFIGURATION                ######\r
-local.clustalo.bin.windows=binaries/windows/clustalo/clustalo.exe\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/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 ram=1700M -l h_cpu=24:00:00  \r
-\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
-## 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 ram=6000M\r
-\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
+#<execname>.jar.file = binaries/windows/bj3.0.4p-jronn.jar\r
+\r
+\r
+\r
+\r
+###########################################################################################\r
+#                             CLUSTAL CONFIGURATION                                       #\r
+###########################################################################################\r
+local.clustalw.bin.windows = binaries/windows/clustalw2.exe\r
+local.clustalw.bin         = binaries/src/clustalw/src/clustalw2\r
+#cluster.clustalw.bin       =/home/jabaws/binaries/src/clustalw/src/clustalw2\r
+### This parameter 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 ram=6000M\r
+\r
+\r
+###########################################################################################\r
+#                             CLUSTAL OMEGA CONFIGURATION                                 #\r
+###########################################################################################\r
+local.clustalo.bin.windows = binaries/windows/clustalo/clustalo.exe\r
+local.clustalo.bin         = binaries/src/clustalo/src/clustalo\r
+#cluster.clustalo.bin       = /home/jabaws/binaries/src/clustalo/src/clustalo\r
+### This parameter specifies the directory where the matrices files are stored\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 run on multiple CPUs on the cluster. This parameter specifies CPU #NN\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 ram=1700M -l h_cpu=24:00:00\r
+\r
+\r
+###########################################################################################\r
+#                               MUSCLE CONFIGURATION                                      #\r
+###########################################################################################\r
+local.muscle.bin.windows = binaries/windows/muscle.exe\r
+local.muscle.bin         = binaries/src/muscle/muscle\r
+#cluster.muscle.bin       = /home/jabaws/binaries/src/muscle/muscle\r
+### This parameter 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 ram=6000M\r
+\r
+\r
+###########################################################################################\r
+#                               MAFFT CONFIGURATION                                       #\r
+###########################################################################################\r
+local.mafft.bin        = binaries/src/mafft/scripts/mafft\r
+#cluster.mafft.bin      = /home/jabaws/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
-#mafft.limits.file=conf/settings/MafftLimits.xml\r
-#mafft.cluster.settings=-l h_cpu=24:00:00 -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
+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
+#mafft.limits.file      = conf/settings/MafftLimits.xml\r
+#mafft.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M\r
+\r
+\r
+###########################################################################################\r
+#                      TCOFFEE CONFIGURATION                                              #\r
+###########################################################################################\r
+local.tcoffee.bin        = binaries/src/tcoffee/t_coffee_source/t_coffee\r
+#cluster.tcoffee.bin      = /home/jabaws/binaries/src/tcoffee/t_coffee_source/t_coffee\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 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 ram=1700M -l h_cpu=24:00:00  \r
-\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.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 ram=6000M\r
-\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
-#ERROR!!! jronn.jar.file=binaries/windows/jronn3.1.jar\r
-jronn.jar.file=binaries/windows/bj3.0.4p-jronn.jar\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_cpu=24:00:00\r
-\r
-\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 ram=6000M\r
-\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 ram=6000M\r
-\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 \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 ram=6000M\r
-\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
-## 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 ram=1700M -l h_cpu=24:00:00\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 can be executed on multiple CPUs if run on the cluster. This parameter defines CPUs #N\r
+#tcoffee.cluster.cpunum   = 4\r
+### This paramer defines queue setting with CPUNUM on the cluster\r
+#tcoffee.cluster.settings = -q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00\r
+\r
+\r
+###########################################################################################\r
+#                      PROBCONS CONFIGURATION                                             #\r
+###########################################################################################\r
+local.probcons.bin         = binaries/src/probcons/probcons\r
+#cluster.probcons.bin       = /home/jabaws/binaries/src/probcons/probcons\r
+probcons.parameters.file   = conf/settings/ProbconsParameters.xml\r
+#probcons.limits.file       = conf/settings/ProbconsLimits.xml\r
+### This parameter defines queue settings for PROBCON on the cluster\r
+#probcons.cluster.settings  = -l h_cpu=24:00:00 -l ram=6000M\r
+\r
+\r
+###########################################################################################\r
+#                      JRONN CONFIGURATION                                                #\r
+###########################################################################################\r
+### If no local path is specified, Java is loaded from JAVA_HOME variable for local \r
+### execution. However, cluster.jronn.bin MUST be specified for 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/bj3.0.4p-jronn.jar\r
+#jronn.limits.file        = conf/settings/JronnLimits.xml\r
+## Jronn can use multiple CPUs. This parameter specifies the number of CPUs\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_cpu=24:00:00\r
+\r
+\r
+###########################################################################################\r
+#                      DISEMBL CONFIGURATION                                              #\r
+###########################################################################################\r
+local.disembl.bin         = binaries/src/disembl/DisEMBL.py\r
+#cluster.disembl.bin       = /home/jabaws/binaries/src/disembl/DisEMBL.py\r
+#disembl.limits.file       = conf/settings/DisemblLimits.xml\r
+#disembl.cluster.settings  = -l h_cpu=24:00:00 -l ram=6000M\r
+\r
+\r
+###########################################################################################\r
+#                      GLOBPLOT CONFIGURATION                                             #\r
+###########################################################################################\r
+local.globplot.bin         = binaries/src/globplot/GlobPlot.py\r
+#cluster.globplot.bin       = /home/jabaws/binaries/src/globplot/GlobPlot.py\r
+#globplot.bin.env           = PYTHONPATH#/home/jabaws/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 ram=6000M\r
+\r
+\r
+###########################################################################################\r
+#                      IUPRED CONFIGURATION                                               #\r
+###########################################################################################\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 \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       = /home/jabaws/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 ram=6000M\r
+\r
+\r
+###########################################################################################\r
+#                       AACON CONFIGURATION                                               #\r
+###########################################################################################\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
+### AACon can use multiple CPUs. This parameter defines the number of CPUs:\r
+#aacon.cluster.cpunum     = 4\r
+### This parameter defines queue settings for AACON on the cluster\r
+#aacon.cluster.settings   = -q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00\r
+\r
+###########################################################################################\r
+#                               MAFFT CONFIGURATION                                       #\r
+###########################################################################################\r
+local.jpred.bin        = binaries/src/jpred/jpred.pl\r
+#cluster.jpred.bin      = /home/jabaws/binaries/src/jpred/jpred.pl\r
+# These paths will be converted to absolute if relative.\r
+jpred.bin.env          = BLASTMAT#binaries/src/jpred/data/blast;UNIREFDB#binaries/src/jpred/unirefdb;\r
+### This parameters specifies the directory where the matrices files are stored\r
+jpred.presets.file     = conf/settings/JpredPresets.xml\r
+jpred.parameters.file  = conf/settings/JpredParameters.xml\r
+#jpred.limits.file      = conf/settings/JpredLimits.xml\r
+#jpred.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M\r

diff --git a/conf/Executable.properties.dundee b/conf/Executable.properties.dundee
new file mode 100644 (file)
index 0000000..8d5c761
--- /dev/null
+++ b/conf/Executable.properties.dundee
@@ -0,0 +1,212 @@
+###########################################################################################
+#                                                                                         #
+#            THIS IS JABAWS EXECUTABLE CONFIGURATION FILE                                 #
+#                                                                                         #
+###########################################################################################
+
+### Properties supported by executables.
+### <execname> is one of the available applications: 
+### [clustalw, mafft, muscle, propcons, tcoffee, iupred, jronn, globplot, disembl, aacon, jpred]
+
+### Path to the native executable on Windows must be either absolute, 
+### or relative to JABAWS web application
+# local.<execname>.bin.windows = binaries/windows/clustalw2.exe
+
+### Path to the native executable not on Windows (e.g. Linux, Mac)
+### must be either absolute, or relative to JABAWS web application
+# local.<execname>.bin = binaries/src/clustalw/src/clustalw2
+
+### Path to the native executable on the cluster (must be accessible from all 
+### cluster nodes which will run JABAWS jobs). The path must be absolute. 
+# cluster.<execname>.bin = /home/jabaws/binaries/src/clustalw/src/clustalw2
+
+### At least one of the path to the native executable should be defined.
+
+### If an application supports presets, the preset file can have either  
+### absolute or relative to the JABAWS web application path to the file. 
+### The file is optional.
+# <execname>.presets.file = conf/settings/ClustalPresets.xml
+
+### If an application supports parameters, the parameter file can have either 
+### absolute or relative to the JABAWS web application path to the file. 
+### The file is optional.
+# <execname>.parameters.file = conf/settings/ClustalParameters.xml
+
+## Application limits, absolute or relative to 
+## the JABAWS web application path to the file. Optional.
+## Use this if you want to limit the size of the job to be accepted by a 
+## Webservice. The limits files we use in Dundee are provided with JABAWS. 
+# <execname>.limits.file=conf/settings/ClustalLimits.xml
+
+## Flags passed to the cluster batch manager for the application. Optional.
+## This example sets a maximum execution time to 24 hours and maximum amount of 
+## memory per task to 6Gb for SGE and OGE cluster batch managers.
+## Please note that all the examples of this parameter below are correct for 
+## Sun Grid Engine or Open Grid Engine (untested) only! If you use a different 
+## batch manager you would need to specify different flags.  
+# <execname>.cluster.settings = -l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
+
+## Environmental variables required by native executables. Optional. 
+## Format: VARIABLE_NAME1#VARIABLE_VALUE1;VARIABLE_NAME2#VARIABLE_VALUE2; 
+# <execname>.bin.env = MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;
+
+## Parameter supported by the executable Jar files, such as jronn and aacon, 
+## point to the location of the jar file. Also, local.<execname>.bin, 
+## local.<execname>.bin.windows properties are optional for these, if not 
+## provided they will be replaced to the java executable path from JAVA_HOME 
+## environmental variable. 
+#<execname>.jar.file = binaries/windows/bj3.0.4p-jronn.jar
+
+
+
+
+###########################################################################################
+#                                  CLUSTAL CONFIGURATION                                  #
+###########################################################################################
+local.clustalw.bin.windows = binaries/windows/clustalw2.exe
+local.clustalw.bin         = binaries/src/clustalw/src/clustalw2
+cluster.clustalw.bin       = /home/jabaws/tomcat/webapps/jabaws/binaries/src/clustalw/src/clustalw2
+### This parameters specifies the directory where the matrices files are stored
+clustalw.-matrix.path      = binaries/matrices
+clustalw.presets.file      = conf/settings/ClustalPresets.xml
+clustalw.parameters.file   = conf/settings/ClustalParameters.xml
+clustalw.limits.file       = conf/settings/ClustalLimits.xml
+clustalw.cluster.settings  = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M
+
+
+###########################################################################################
+#                                  CLUSTAL OMEGA CONFIGURATION                            #
+###########################################################################################
+local.clustalo.bin.windows = binaries/windows/clustalo/clustalo.exe
+local.clustalo.bin         = binaries/src/clustalo/src/clustalo
+cluster.clustalo.bin       = /home/jabaws/tomcat/webapps/jabaws/binaries/src/clustalo/src/clustalo
+### This parameters specifies the directory where the matrices files are stored
+#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. This parameter specifies the number of CPUs:
+clustalo.cluster.cpunum    = 4
+### This reserves a slot with CPUNUM on the cluster for the task
+clustalo.cluster.settings  = -P webservices -R y -q 64bit-pri.q -pe smp 4 -l ram=3400M -l h_cpu=24:00:00
+
+
+###########################################################################################
+#                                  MUSCLE CONFIGURATION                                   #
+###########################################################################################
+local.muscle.bin.windows = binaries/windows/muscle.exe
+local.muscle.bin         = binaries/src/muscle/muscle
+cluster.muscle.bin       = /home/jabaws/tomcat/webapps/jabaws/binaries/src/muscle/muscle
+### This parameters specifies the directory where the matrices files are stored
+muscle.-matrix.path      = binaries/matrices
+muscle.presets.file      = conf/settings/MusclePresets.xml
+muscle.parameters.file   = conf/settings/MuscleParameters.xml
+muscle.limits.file       = conf/settings/MuscleLimits.xml
+muscle.cluster.settings  = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M
+
+
+###########################################################################################
+#                                  MAFFT CONFIGURATION                                    #
+###########################################################################################
+local.mafft.bin         = binaries/src/mafft/scripts/mafft
+cluster.mafft.bin       = /home/jabaws/tomcat/webapps/jabaws/binaries/src/mafft/scripts/mafft
+# These paths will be converted to absolute if relative.
+mafft.bin.env           = MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;
+### This parameters specifies the directory where the matrices files are stored
+mafft.--aamatrix.path   = binaries/matrices
+mafft.presets.file      = conf/settings/MafftPresets.xml
+mafft.parameters.file   = conf/settings/MafftParameters.xml
+mafft.limits.file       = conf/settings/MafftLimits.xml
+mafft.cluster.settings  = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M
+
+
+###########################################################################################
+#                                  TCOFFEE CONFIGURATION                                  #
+###########################################################################################
+local.tcoffee.bin         = binaries/src/tcoffee/t_coffee_source/t_coffee
+cluster.tcoffee.bin       = /home/jabaws/tomcat/webapps/jabaws/binaries/src/tcoffee/t_coffee_source/t_coffee
+# This variable is required by tcoffee
+tcoffee.bin.env           = HOME_4_TCOFFEE#jobsout;
+tcoffee.presets.file      = conf/settings/TcoffeePresets.xml
+tcoffee.parameters.file   = conf/settings/TcoffeeParameters.xml
+tcoffee.limits.file       = conf/settings/TcoffeeLimits.xml
+### Tcoffee can be executed on multiple CPUs. This parameter specifies the number of CPUs:
+tcoffee.cluster.cpunum    = 4
+### This reserves a slot with CPUNUM on the cluster for the task
+tcoffee.cluster.settings  = -P webservices -R y -q 64bit-pri.q -pe smp 4 -l ram=3400M -l h_cpu=24:00:00
+
+
+###########################################################################################
+#                                  PROBCONS CONFIGURATION                                 #
+###########################################################################################
+local.probcons.bin         = binaries/src/probcons/probcons
+cluster.probcons.bin       = /home/jabaws/tomcat/webapps/jabaws/binaries/src/probcons/probcons
+probcons.parameters.file   = conf/settings/ProbconsParameters.xml
+probcons.limits.file       = conf/settings/ProbconsLimits.xml
+probcons.cluster.settings  = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M
+
+
+###########################################################################################
+#                                  JRONN CONFIGURATION                                    #
+###########################################################################################
+### If no local path is specified, Java is loaded from JAVA_HOME variable for local 
+### execution. However, cluster.jronn.bin MUST be specified for running Jronn on the cluster.
+#local.jronn.bin.windows  = D:\\Java\\jdk1.6.0_24\\bin\\java.exe 
+local.jronn.bin          = /home/jabaws/java/jdk/bin/java
+cluster.jronn.bin        = /home/jabaws/java/jdk/bin/java
+jronn.jar.file           = binaries/windows/bj3.0.4p-jronn.jar
+jronn.limits.file        = conf/settings/JronnLimits.xml
+### Jronn can use multiple CPUs. This parameter specifies the number of CPU:
+jronn.cluster.cpunum     = 4
+### This reserves a slot with CPUNUM on the cluster for the task
+jronn.cluster.settings   = -P webservices -R y -q 64bit-pri.q -pe smp 4 -l h_cpu=24:00:00
+
+
+###########################################################################################
+#                                  DISEMBL CONFIGURATION                                  #
+###########################################################################################
+local.disembl.bin        = binaries/src/disembl/DisEMBL.py
+cluster.disembl.bin      = /home/jabaws/tomcat/webapps/jabaws/binaries/src/disembl/DisEMBL.py
+disembl.limits.file      = conf/settings/DisemblLimits.xml
+disembl.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M
+
+
+###########################################################################################
+#                                  GLOBPLOT CONFIGURATION                                 #
+###########################################################################################
+local.globplot.bin        = binaries/src/globplot/GlobPlot.py
+cluster.globplot.bin      = /home/jabaws/tomcat/webapps/jabaws/binaries/src/globplot/GlobPlot.py
+globplot.bin.env          = PYTHONPATH#/home/jabaws/tomcat/webapps/jabaws/binaries/src/globplot/biopython-1.50
+globplot.limits.file      = conf/settings/GlobPlotLimits.xml
+globplot.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M
+
+
+###########################################################################################
+#                                 IUPRED CONFIGURATION                                    #
+###########################################################################################
+local.iupred.bin.windows = binaries/windows/iupred/iupred.exe 
+local.iupred.bin         = binaries/src/iupred/iupred
+### This must point to the directory where iupred binary is, with other files it 
+### depends on. This path will be converted to absolute if relative at runtime. 
+iupred.bin.env           = IUPred_PATH#binaries/src/iupred
+cluster.iupred.bin       = /home/jabaws/tomcat/webapps/jabaws/binaries/src/iupred/iupred
+iupred.parameters.file   = conf/settings/IUPredParameters.xml
+iupred.limits.file       = conf/settings/IUPredLimits.xml
+iupred.cluster.settings  = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M
+
+
+###########################################################################################
+#                                  AACON CONFIGURATION                                    #
+###########################################################################################
+### This is just a path to the standard java executable 
+local.aacon.bin          = /home/jabaws/java/jdk/bin/java
+cluster.aacon.bin        = /home/jabaws/java/jdk/bin/java
+### Path to the AACon library
+aacon.jar.file           = binaries/windows/aaconservation.jar
+aacon.parameters.file    = conf/settings/AAConParameters.xml
+aacon.presets.file       = conf/settings/AAConPresets.xml
+aacon.limits.file        = conf/settings/AAConLimits.xml
+### AACon can use multiple CPUs
+### This parameter specifies the number of CPUs to use
+aacon.cluster.cpunum     = 4
+### This reserves a slot with CPUNUM on the cluster for the task
+aacon.cluster.settings   = -P webservices -R y -q 64bit-pri.q -pe smp 4 -l ram=3400M -l h_cpu=24:00:00