X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=conf%2FExecutable.properties;h=a592c3af4625e5ff27d44a26d8c125d005f12a3e;hb=5041367ba7b1ad4a56d2c64e5bf2734cbc45bf4e;hp=11a4f246cb2a970295766ce800b652f4431f23d6;hpb=4a317845b7f26b5e93bd4d9f5ec350083d3e35b0;p=jabaws.git diff --git a/conf/Executable.properties b/conf/Executable.properties index 11a4f24..a592c3a 100644 --- a/conf/Executable.properties +++ b/conf/Executable.properties @@ -61,7 +61,7 @@ ########################################################################################### -# CLUSTAL CONFIGURATION # +# CLUSTAL W CONFIGURATION # ########################################################################################### local.clustalw.bin.windows = binaries/windows/clustalw2.exe local.clustalw.bin = binaries/src/clustalw/src/clustalw2 @@ -70,7 +70,7 @@ local.clustalw.bin = binaries/src/clustalw/src/clustalw2 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.limits.file = conf/settings/ClustalLimits.xml #clustalw.cluster.settings =-l h_cpu=24:00:00 -l ram=6000M @@ -83,7 +83,7 @@ local.clustalo.bin = binaries/src/clustalo/src/clustalo ### This parameter 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.limits.file = conf/settings/ClustaloLimits.xml ### ClustalO can be run on multiple CPUs on the cluster. This parameter specifies CPU #NN clustalo.cluster.cpunum = 4 ### This reserves a slot with CPUNUM on the cluster for the task @@ -100,7 +100,7 @@ local.muscle.bin = binaries/src/muscle/muscle 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.limits.file = conf/settings/MuscleLimits.xml #muscle.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M @@ -115,7 +115,7 @@ mafft.bin.env = MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFF 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.limits.file = conf/settings/MafftLimits.xml #mafft.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M @@ -128,7 +128,7 @@ local.tcoffee.bin = binaries/src/tcoffee/t_coffee_source/t_coffee 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.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 @@ -141,7 +141,7 @@ tcoffee.parameters.file = conf/settings/TcoffeeParameters.xml local.probcons.bin = binaries/src/probcons/probcons #cluster.probcons.bin = /home/jabaws/binaries/src/probcons/probcons probcons.parameters.file = conf/settings/ProbconsParameters.xml -#probcons.limits.file = conf/settings/ProbconsLimits.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 @@ -155,7 +155,7 @@ probcons.parameters.file = conf/settings/ProbconsParameters.xml #local.jronn.bin = /sw/java/latest/bin/java #cluster.jronn.bin = /sw/java/latest/bin/java jronn.jar.file = binaries/windows/bj3.0.4p-jronn.jar -#jronn.limits.file = conf/settings/JronnLimits.xml +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 @@ -167,7 +167,7 @@ jronn.jar.file = binaries/windows/bj3.0.4p-jronn.jar ########################################################################################### 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.limits.file = conf/settings/DisemblLimits.xml #disembl.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M @@ -191,7 +191,7 @@ local.iupred.bin = binaries/src/iupred/iupred iupred.bin.env = IUPred_PATH#binaries/src/iupred #cluster.iupred.bin = /home/jabaws/binaries/src/iupred/iupred iupred.parameters.file = conf/settings/IUPredParameters.xml -#iupred.limits.file = conf/settings/IUPredLimits.xml +iupred.limits.file = conf/settings/IUPredLimits.xml #iupred.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M @@ -206,7 +206,7 @@ iupred.parameters.file = conf/settings/IUPredParameters.xml 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.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 @@ -225,3 +225,15 @@ 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 + +########################################################################################### +# 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 +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 + +