JWS-114 Commented out ‘cluster’ entries for consistency with other methods.

[jabaws.git] / conf / Executable.properties

diff --git a/conf/Executable.properties b/conf/Executable.properties
index 11a4f24..2bdc9a2 100644 (file)
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -61,7 +61,7 @@
 \r
 \r
 ###########################################################################################\r
-#                             CLUSTAL CONFIGURATION                                       #\r
+#                             CLUSTAL W CONFIGURATION                                     #\r
 ###########################################################################################\r
 local.clustalw.bin.windows = binaries/windows/clustalw2.exe\r
 local.clustalw.bin         = binaries/src/clustalw/src/clustalw2\r
@@ -70,7 +70,7 @@ local.clustalw.bin         = binaries/src/clustalw/src/clustalw2
 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.limits.file      = conf/settings/ClustalLimits.xml\r
 #clustalw.cluster.settings =-l h_cpu=24:00:00 -l ram=6000M\r
 \r
 \r
@@ -83,7 +83,7 @@ local.clustalo.bin         = binaries/src/clustalo/src/clustalo
 ### 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.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
@@ -100,7 +100,7 @@ local.muscle.bin         = binaries/src/muscle/muscle
 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.limits.file       = conf/settings/MuscleLimits.xml\r
 #muscle.cluster.settings  = -l h_cpu=24:00:00 -l ram=6000M\r
 \r
 \r
@@ -115,7 +115,7 @@ mafft.bin.env          = MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFF
 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.limits.file      = conf/settings/MafftLimits.xml\r
 #mafft.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M\r
 \r
 \r
@@ -128,7 +128,7 @@ local.tcoffee.bin        = binaries/src/tcoffee/t_coffee_source/t_coffee
 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.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
@@ -141,7 +141,7 @@ tcoffee.parameters.file  = conf/settings/TcoffeeParameters.xml
 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
+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
@@ -155,7 +155,7 @@ probcons.parameters.file   = conf/settings/ProbconsParameters.xml
 #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.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
@@ -167,7 +167,7 @@ jronn.jar.file           = binaries/windows/bj3.0.4p-jronn.jar
 ###########################################################################################\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.limits.file       = conf/settings/DisemblLimits.xml\r
 #disembl.cluster.settings  = -l h_cpu=24:00:00 -l ram=6000M\r
 \r
 \r
@@ -191,7 +191,7 @@ local.iupred.bin         = binaries/src/iupred/iupred
 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.limits.file       = conf/settings/IUPredLimits.xml\r
 #iupred.cluster.settings  = -l h_cpu=24:00:00 -l ram=6000M\r
 \r
 \r
@@ -206,7 +206,7 @@ iupred.parameters.file   = conf/settings/IUPredParameters.xml
 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.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
@@ -215,13 +215,47 @@ aacon.presets.file       = conf/settings/AAConPresets.xml
 ###########################################################################################\r
 #                               JPRED 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.cpunum   = 4\r
-#jpred.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M\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\r
+## The varible jpred.data.uniref.path define a path to Uniref90 files used by Jpred. If\r
+## you install the database to a different path chenge the variable here\r
+#jpred.data.uniref.path = /data/UNIREFdb\r
+## WARNING!!!\r
+## Redefine jpred.data.uniref.name if you do undestand what the variable means\r
+#jpred.data.uniref.name = cluster\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.cpunum   = 4\r
+##jpred.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M\r
+\r
+###########################################################################################\r
+#                               RNAALIFOLD CONFIGURATION                                  #\r
+###########################################################################################\r
+local.rnaalifold.bin.windows = binaries/windows/ViennaRNA/RNAalifold.exe\r
+local.rnaalifold.bin         = binaries/src/ViennaRNA/Progs/RNAalifold\r
+#cluster.rnaalifold.bin      = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/ViennaRNA/Progs/RNAalifold\r
+rnaalifold.parameters.file   = conf/settings/RNAalifoldParameters.xml\r
+rnaalifold.limits.file       = conf/settings/RNAalifoldLimits.xml\r
+#rnaalifold.cluster.settings  = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M\r
+\r
+###########################################################################################\r
+#                                 MSAProbs CONFIGURATION                                  #\r
+###########################################################################################\r
+local.msaprobs.bin         = binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs\r
+#cluster.msaprobs.bin       = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs\r
+msaprobs.parameters.file   = conf/settings/MSAprobsParameters.xml\r
+msaprobs.limits.file       = conf/settings/MSAprobsLimits.xml\r
+#msaprobs.cluster.settings  = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M\r
+\r
+###########################################################################################\r
+#                                  GLprobs CONFIGURATION                                  #\r
+###########################################################################################\r
+local.glprobs.bin         = binaries/src/GLProbs-1.0/glprobs\r
+#cluster.glprobs.bin       = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/GLProbs-1.0/glprobs\r
+glprobs.parameters.file   = conf/settings/GLprobsParameters.xml\r
+glprobs.limits.file       = conf/settings/GLprobsLimits.xml\r
+#glprobs.cluster.settings  = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M\r