From: Fábio Madeira Date: Wed, 12 Apr 2017 16:47:49 +0000 (+0100) Subject: JWS-114 Fixed what the default for local and cluster should (also considering people... X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fc64881a049afa95bf13aa9a7e684000136e0244;p=jabaws.git JWS-114 Fixed what the default for local and cluster should (also considering people not running jabaws in Dundee) --- diff --git a/conf/Engine.cluster.properties b/conf/Engine.cluster.properties index 3036b61..7b527b7 100644 --- a/conf/Engine.cluster.properties +++ b/conf/Engine.cluster.properties @@ -1,7 +1,7 @@ ################################################################################# # enable or disable engine true | false # OPTIONAL defaults to false -engine.cluster.enable=true +engine.cluster.enable=false ################################################################################# # Directory to use for temporary files storage diff --git a/conf/Engine.local.properties b/conf/Engine.local.properties index 486edb2..1f54acb 100644 --- a/conf/Engine.local.properties +++ b/conf/Engine.local.properties @@ -8,8 +8,7 @@ engine.local.enable=true # OPTIONAL defaults to java temporary directory # Relative path within the project will be converted in absolute at runtime #local.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/local_jobsout -###local.tmp.directory=jobsout -local.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/local_jobsout +local.tmp.directory=jobsout ################################################################################# # Number of threads for tasks execution (valid values between 1 and 2x cpu. diff --git a/conf/Executable.properties.dundee b/conf/Executable.properties.dundee index 079cded..d11fdc3 100644 --- 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