JWS-114 Fixed what the default for local and cluster should (also considering people...

diff --git a/conf/Engine.cluster.properties b/conf/Engine.cluster.properties
index 3036b61..7b527b7 100644 (file)
--- a/conf/Engine.cluster.properties
+++ b/conf/Engine.cluster.properties
@@ -1,7 +1,7 @@
 #################################################################################\r
 # enable or disable engine true | false\r
 # OPTIONAL defaults to false\r
-engine.cluster.enable=true\r
+engine.cluster.enable=false\r
 \r
 #################################################################################\r
 # Directory to use for temporary files storage\r

diff --git a/conf/Engine.local.properties b/conf/Engine.local.properties
index 486edb2..1f54acb 100644 (file)
--- a/conf/Engine.local.properties
+++ b/conf/Engine.local.properties
@@ -8,8 +8,7 @@ engine.local.enable=true
 # OPTIONAL defaults to java temporary directory \r
 # Relative path within the project will be converted in absolute at runtime\r
 #local.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/local_jobsout \r
-###local.tmp.directory=jobsout\r
-local.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/local_jobsout\r
+local.tmp.directory=jobsout\r
 \r
 #################################################################################\r
 # Number of threads for tasks execution (valid values between 1 and 2x cpu.\r

diff --git a/conf/Executable.properties.dundee b/conf/Executable.properties.dundee
index 079cded..d11fdc3 100644 (file)
--- a/conf/Executable.properties.dundee
+++ b/conf/Executable.properties.dundee
@@ -76,7 +76,7 @@ clustalw.cluster.settings  = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_
 ###########################################################################################
 local.clustalo.bin.windows = binaries/windows/clustalo/clustalo.exe
 local.clustalo.bin         = binaries/src/clustalo/src/clustalo
-cluster.clustalo.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/clustalo/src/clustalo
+cluster.clustalo.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/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
@@ -92,7 +92,7 @@ clustalo.cluster.settings  = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe s
 ###########################################################################################
 local.muscle.bin.windows = binaries/windows/muscle.exe
 local.muscle.bin         = binaries/src/muscle/muscle
-cluster.muscle.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/muscle/muscle
+cluster.muscle.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/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
@@ -105,7 +105,7 @@ muscle.cluster.settings  = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cp
 #                                  MAFFT CONFIGURATION                                    #
 ###########################################################################################
 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
+cluster.mafft.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/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
@@ -120,7 +120,7 @@ mafft.cluster.settings  = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu
 #                                  TCOFFEE CONFIGURATION                                  #
 ###########################################################################################
 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
+cluster.tcoffee.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/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
@@ -136,7 +136,7 @@ tcoffee.cluster.settings  = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe sm
 #                                  PROBCONS CONFIGURATION                                 #
 ###########################################################################################
 local.probcons.bin         = 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
+cluster.probcons.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/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 -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M
@@ -162,7 +162,7 @@ jronn.cluster.settings   = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp
 #                                  DISEMBL CONFIGURATION                                  #
 ###########################################################################################
 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
+cluster.disembl.bin      = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/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
 
@@ -171,8 +171,8 @@ disembl.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cp
 #                                  GLOBPLOT CONFIGURATION                                 #
 ###########################################################################################
 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
+cluster.globplot.bin      = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/globplot/GlobPlot.py
+globplot.bin.env          = PYTHONPATH#/homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/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
 
@@ -185,7 +185,7 @@ 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       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/iupred/iupred
+cluster.iupred.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/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 -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M
@@ -212,7 +212,7 @@ aacon.cluster.settings   = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp
 #                               JPRED CONFIGURATION                                       #
 ###########################################################################################
 #local.jpred.bin        = 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
+#cluster.jpred.bin      = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/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
@@ -233,7 +233,7 @@ aacon.cluster.settings   = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp
 ###########################################################################################
 local.rnaalifold.bin.windows = binaries/windows/ViennaRNA/RNAalifold.exe
 local.rnaalifold.bin         = 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
+cluster.rnaalifold.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/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 -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M
@@ -242,7 +242,7 @@ rnaalifold.cluster.settings  = -P webservices -R y -q 64bit-pri.q -q c6100.q -l
 #                                 MSAProbs CONFIGURATION                                  #
 ###########################################################################################
 local.msaprobs.bin         = 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
+cluster.msaprobs.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/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 -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M
@@ -251,7 +251,7 @@ msaprobs.cluster.settings  = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_
 #                                  GLprobs CONFIGURATION                                  #
 ###########################################################################################
 local.glprobs.bin         = 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
+cluster.glprobs.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/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 -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M