X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=conf%2FExecutable.properties;h=ac2fb9dafdf00dfd512164fed4adf4e530356745;hb=2c116eabb17f6a2b80b9cf8d91770a7e67042fc1;hp=2bdc9a217e3481871a42dde3901606643220e9cd;hpb=d8904b59aa3bc76d88529e63a690a6801ef794c8;p=jabaws.git diff --git a/conf/Executable.properties b/conf/Executable.properties index 2bdc9a2..ac2fb9d 100644 --- a/conf/Executable.properties +++ b/conf/Executable.properties @@ -5,10 +5,10 @@ ########################################################################################### ### Properties supported by executables. -### is one of the available applications: +### 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, +### Path to the native executable on Windows must be either absolute, ### or relative to JABAWS web application # local..bin.windows = binaries/windows/clustalw2.exe @@ -16,212 +16,208 @@ ### must be either absolute, or relative to JABAWS web application # local..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. +### 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..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. +### 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. # .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. +### 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. # .parameters.file = conf/settings/ClustalParameters.xml -## Application limits, absolute or relative to +## 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. +## 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. # .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. +## 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. # .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; +## Environmental variables required by native executables. Optional. +## Format: VARIABLE_NAME1#VARIABLE_VALUE1;VARIABLE_NAME2#VARIABLE_VALUE2; # .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..bin, -## local..bin.windows properties are optional for these, if not -## provided they will be replaced to the java executable path from JAVA_HOME -## environmental variable. +## Parameter supported by the executable Jar files, such as jronn and aacon, +## point to the location of the jar file. Also, local..bin, +## local..bin.windows properties are optional for these, if not +## provided they will be replaced to the java executable path from JAVA_HOME +## environmental variable. #.jar.file = binaries/windows/bj3.0.4p-jronn.jar - - - ########################################################################################### # CLUSTAL W CONFIGURATION # ########################################################################################### local.clustalw.bin.windows = binaries/windows/clustalw2.exe local.clustalw.bin = binaries/src/clustalw/src/clustalw2 -#cluster.clustalw.bin =/home/jabaws/binaries/src/clustalw/src/clustalw2 -### This parameter specifies the directory where the matrices files are stored +cluster.clustalw.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/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 =-l h_cpu=24:00:00 -l ram=6000M +clustalw.limits.file = conf/settings/ClustalLimits.xml +clustalw.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### -# CLUSTAL OMEGA CONFIGURATION # +# 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/binaries/src/clustalo/src/clustalo -### This parameter specifies the directory where the matrices files are stored +cluster.clustalo.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/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 run on multiple CPUs on the cluster. This parameter specifies CPU #NN +### 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 = -q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00 +### This reserves a slot with CPUNUM on the Cluster for the task +clustalo.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=3400M ########################################################################################### -# MUSCLE CONFIGURATION # +# MUSCLE CONFIGURATION # ########################################################################################### local.muscle.bin.windows = binaries/windows/muscle.exe local.muscle.bin = binaries/src/muscle/muscle -#cluster.muscle.bin = /home/jabaws/binaries/src/muscle/muscle -### This parameter specifies the directory where the matrices files are stored +cluster.muscle.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/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 = -l h_cpu=24:00:00 -l ram=6000M +muscle.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### -# MAFFT CONFIGURATION # +# MAFFT CONFIGURATION # ########################################################################################### -local.mafft.bin = binaries/src/mafft/scripts/mafft -#cluster.mafft.bin = /home/jabaws/binaries/src/mafft/scripts/mafft +local.mafft.bin = binaries/src/mafft/scripts/mafft +cluster.mafft.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/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; +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 = -l h_cpu=24:00:00 -l ram=6000M +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 -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### -# TCOFFEE CONFIGURATION # +# TCOFFEE CONFIGURATION # ########################################################################################### -local.tcoffee.bin = binaries/src/tcoffee/t_coffee_source/t_coffee -#cluster.tcoffee.bin = /home/jabaws/binaries/src/tcoffee/t_coffee_source/t_coffee +local.tcoffee.bin = binaries/src/tcoffee/t_coffee_source/t_coffee +cluster.tcoffee.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/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 if run on the cluster. This parameter defines CPUs #N -#tcoffee.cluster.cpunum = 4 -### This paramer defines queue setting with CPUNUM on the cluster -#tcoffee.cluster.settings = -q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00 +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 -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=3400M ########################################################################################### -# PROBCONS CONFIGURATION # +# PROBCONS CONFIGURATION # ########################################################################################### local.probcons.bin = binaries/src/probcons/probcons -#cluster.probcons.bin = /home/jabaws/binaries/src/probcons/probcons +cluster.probcons.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/probcons/probcons probcons.parameters.file = conf/settings/ProbconsParameters.xml probcons.limits.file = conf/settings/ProbconsLimits.xml -### This parameter defines queue settings for PROBCON on the cluster -#probcons.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M +probcons.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### -# JRONN CONFIGURATION # +# 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 = /sw/java/latest/bin/java -#cluster.jronn.bin = /sw/java/latest/bin/java +### 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 = /homes/www-jws2/java/jdk/bin/java +cluster.jronn.bin = /homes/www-jws2/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 CPUs -#jronn.cluster.cpunum = 4 -### This reserves a slot with CPUNUM on the cluster for the task -#jronn.cluster.settings = -q 64bit-pri.q -pe smp 4 -l h_cpu=24:00:00 +### 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 -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### -# DISEMBL CONFIGURATION # +# DISEMBL CONFIGURATION # ########################################################################################### -local.disembl.bin = binaries/src/disembl/DisEMBL.py -#cluster.disembl.bin = /home/jabaws/binaries/src/disembl/DisEMBL.py -disembl.limits.file = conf/settings/DisemblLimits.xml -#disembl.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M +local.disembl.bin = binaries/src/disembl/DisEMBL.py +cluster.disembl.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/disembl/DisEMBL.py +disembl.limits.file = conf/settings/DisemblLimits.xml +disembl.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### -# GLOBPLOT CONFIGURATION # +# GLOBPLOT CONFIGURATION # ########################################################################################### -local.globplot.bin = binaries/src/globplot/GlobPlot.py -#cluster.globplot.bin = /home/jabaws/binaries/src/globplot/GlobPlot.py -#globplot.bin.env = PYTHONPATH#/home/jabaws/binaries/src/globplot/biopython-1.50 -globplot.limits.file = conf/settings/GlobPlotLimits.xml -#globplot.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M +local.globplot.bin = binaries/src/globplot/GlobPlot.py +cluster.globplot.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/globplot/GlobPlot.py +globplot.bin.env = PYTHONPATH#/homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/globplot/biopython-1.50 +globplot.limits.file = conf/settings/GlobPlotLimits.xml +globplot.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### -# IUPRED CONFIGURATION # +# IUPRED CONFIGURATION # ########################################################################################### -local.iupred.bin.windows = binaries/windows/iupred/iupred.exe +#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. +### 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/binaries/src/iupred/iupred +cluster.iupred.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/iupred/iupred iupred.parameters.file = conf/settings/IUPredParameters.xml iupred.limits.file = conf/settings/IUPredLimits.xml -#iupred.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M +iupred.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### -# AACON CONFIGURATION # +# AACON CONFIGURATION # ########################################################################################### -### This is just a path to the standard java executable -#local.aacon.bin.windows = D:\\Java\\jdk1.6.0_24\\bin\\java.exe -#local.aacon.bin = /sw/java/latest/bin/java -#cluster.aacon.bin = /sw/java/latest/bin/java +### This is just a path to the standard java executable +local.aacon.bin = /homes/www-jws2/java/jdk/bin/java +cluster.aacon.bin = /homes/www-jws2/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 defines the number of CPUs: -#aacon.cluster.cpunum = 4 -### This parameter defines queue settings for AACON on the cluster -#aacon.cluster.settings = -q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00 +### 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 -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=3400M ########################################################################################### # JPRED CONFIGURATION # ########################################################################################### #local.jpred.bin = binaries/src/jpred/jpred.pl -##cluster.jpred.bin = /home/jabaws/binaries/src/jpred/jpred.pl +#cluster.jpred.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/jpred/jpred.pl ## These paths will be converted to absolute if relative. #jpred.bin.env = BLASTMAT#binaries/src/jpred/data/blast ## The varible jpred.data.uniref.path define a path to Uniref90 files used by Jpred. If ## you install the database to a different path chenge the variable here -#jpred.data.uniref.path = /data/UNIREFdb +#jpred.data.uniref.path = /homes/www-jpred/databases ## WARNING!!! ## Redefine jpred.data.uniref.name if you do undestand what the variable means #jpred.data.uniref.name = cluster @@ -230,32 +226,32 @@ aacon.limits.file = conf/settings/AAConLimits.xml #jpred.parameters.file = conf/settings/JpredParameters.xml #jpred.limits.file = conf/settings/JpredLimits.xml #jpred.cluster.cpunum = 4 -##jpred.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M +#jpred.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=8000M ########################################################################################### # RNAALIFOLD CONFIGURATION # ########################################################################################### local.rnaalifold.bin.windows = binaries/windows/ViennaRNA/RNAalifold.exe local.rnaalifold.bin = binaries/src/ViennaRNA/Progs/RNAalifold -#cluster.rnaalifold.bin = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/ViennaRNA/Progs/RNAalifold +cluster.rnaalifold.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/ViennaRNA/Progs/RNAalifold rnaalifold.parameters.file = conf/settings/RNAalifoldParameters.xml rnaalifold.limits.file = conf/settings/RNAalifoldLimits.xml -#rnaalifold.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M +rnaalifold.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### # MSAProbs CONFIGURATION # ########################################################################################### local.msaprobs.bin = binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs -#cluster.msaprobs.bin = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs +cluster.msaprobs.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs msaprobs.parameters.file = conf/settings/MSAprobsParameters.xml msaprobs.limits.file = conf/settings/MSAprobsLimits.xml -#msaprobs.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M +msaprobs.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### # GLprobs CONFIGURATION # ########################################################################################### local.glprobs.bin = binaries/src/GLProbs-1.0/glprobs -#cluster.glprobs.bin = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/GLProbs-1.0/glprobs +cluster.glprobs.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/GLProbs-1.0/glprobs glprobs.parameters.file = conf/settings/GLprobsParameters.xml glprobs.limits.file = conf/settings/GLprobsLimits.xml -#glprobs.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M +glprobs.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M