\r
### Clustal configuration ###\r
-local.clustalw.bin.windows=binaries/clustalw2.exe\r
+local.clustalw.bin.windows=binaries/windows/clustalw2.exe\r
local.clustalw.bin=binaries/src/clustalw/src/clustalw2\r
-cluster.clustalw.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/clustalw/src/clustalw2\r
+cluster.clustalw.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalw/src/clustalw2\r
# Parameters names which come from RunnerConfig -> Parameters.xml file ultimately are all lowercased in comparison!\r
# see engine.client.Util.getExecProperty() method for details \r
# So they are case insensitive. \r
clustalw.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
\r
### Muscle configuration ###\r
-local.muscle.bin.windows=binaries/muscle.exe\r
+local.muscle.bin.windows=binaries/windows/muscle.exe\r
local.muscle.bin=binaries/src/muscle/muscle\r
# Beware version of muscle on the cluster older and does not support some \r
# of the newer version attributed thus, will not work with Muscle.java wrapper!\r
-cluster.muscle.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/muscle/muscle\r
+cluster.muscle.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/muscle/muscle\r
#The environment variable MUSCLE_MXPATH can be used to specify a path where the matrices are stored\r
# e.g. MUSCLE_MXPATH#binaries/matrices - but need to privide absolute path!\r
muscle.-matrix.path=binaries/matrices\r
\r
### Mafft configuration ###\r
#local.mafft.bin.windows=\r
-local.mafft.bin=binaries/src/mafft/binaries/mafft\r
-cluster.mafft.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/mafft/binaries/mafft\r
-mafft.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#/sw/bin/fasta34;\r
+local.mafft.bin=binaries/src/mafft/scripts/mafft\r
+cluster.mafft.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/mafft/scripts/mafft\r
+# These paths will be converted to absolute if relative.\r
+mafft.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;\r
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.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
\r
+\r
### Tcoffee configuration ###\r
local.tcoffee.bin=binaries/src/tcoffee/t_coffee_source/t_coffee\r
-cluster.tcoffee.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/tcoffee/t_coffee_source/t_coffee\r
+cluster.tcoffee.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/tcoffee/t_coffee_source/t_coffee\r
#/sw/bin/t_coffee\r
# Sub matrix support does not work \r
#tcoffee.-matrix.path=binaries/matrices\r
+# This variable is required by tcoffee\r
+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
### Probcons configuration ###\r
#local.probcons.bin.windows=\r
local.probcons.bin=binaries/src/probcons/probcons\r
-cluster.probcons.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/probcons/probcons\r
+cluster.probcons.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/probcons/probcons\r
#Probcons does not support matrix loading - unrecognised option reported! \r
probcons.parameters.file=conf/settings/ProbconsParameters.xml\r
probcons.limits.file=conf/settings/ProbconsLimits.xml\r
probcons.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+\r
+### Jronn configuration ### \r
+local.jronn.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe \r
+local.jronn.bin=/sw/java/latest/bin/java\r
+cluster.jronn.bin=/sw/java/latest/bin/java\r
+jronn.jar.file=binaries/windows/jronn3.1.jar\r
+# jronn.parameters.file=conf/settings/JronnParameters.xml\r
+jronn.limits.file=conf/settings/JronnLimits.xml\r
+#TODO jronn.jvm.options=-Xms32M -Xmx512M\r
+jronn.cluster.cpunum=4\r
+jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00\r
+\r
+\r
+### Disembl configuration Tisean - Disembl dependancy ### \r
+#local.disembl.bin.windows= \r
+local.disembl.bin=binaries/src/disembl/DisEMBL.py\r
+cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py\r
+# disembl.parameters.file=conf/settings/DisemblParameters.xml\r
+disembl.limits.file=conf/settings/DisemblLimits.xml\r
+disembl.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+\r
+### GlobPlot configuration Tisean - GlobPlot and Disembl dependancy ### \r
+#local.disembl.bin.windows= \r
+local.globplot.bin=binaries/src/globplot/GlobPlot.py\r
+cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/GlobPlot.py\r
+# Dundee only settings\r
+globplot.bin.env=PYTHONPATH#/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/biopython-1.50 \r
+# globplot.parameters.file=conf/settings/GlobPlotParameters.xml\r
+globplot.limits.file=conf/settings/GlobPlotLimits.xml\r
+globplot.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+\r
+### IUPred configuration ### \r
+local.iupred.bin.windows=binaries/windows/iupred/iupred.exe \r
+local.iupred.bin=binaries/src/iupred/iupred\r
+# This must point to the directory where iupred binary is, with other files it depends on\r
+#iupred.bin.env=IUPred_PATH#/homes/pvtroshin/workspace/jaba2/binaries/src/iupred\r
+# This path will be converted to absolute if relative. \r
+iupred.bin.env=IUPred_PATH#binaries/src/iupred\r
+cluster.iupred.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/iupred/iupred\r
+iupred.parameters.file=conf/settings/IUPredParameters.xml\r
+iupred.limits.file=conf/settings/IUPredLimits.xml\r
+iupred.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+\r
+### AACon configuration ###\r
+# This is just a path to the standard java executable \r
+local.aacon.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe \r
+local.aacon.bin=/sw/java/latest/bin/java\r
+cluster.aacon.bin=/sw/java/latest/bin/java\r
+# Path to the AACon library\r
+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
+#TODO jronn.jvm.options=-Xms32M -Xmx512M\r
+aacon.cluster.cpunum=4\r
git://source.jalview.org / jabaws.git / blobdiff