Revert multithreading support for mafft as it does not seem to work

[jabaws.git] / conf / Executable.properties

diff --git a/conf/Executable.properties b/conf/Executable.properties
index d621a3b..7ee672f 100644 (file)
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -1,6 +1,6 @@
 \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/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
@@ -13,7 +13,7 @@ clustalw.limits.file=conf/settings/ClustalLimits.xml
 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
@@ -28,8 +28,9 @@ muscle.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
 \r
 ### Mafft configuration ###\r
 #local.mafft.bin.windows=\r
-local.mafft.bin=binaries/src/mafft/binaries/mafft\r
-cluster.mafft.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/mafft/core/mafft\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
@@ -37,6 +38,7 @@ mafft.parameters.file=conf/settings/MafftParameters.xml
 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/pvtroshin/workspace/jaba2/binaries/src/tcoffee/t_coffee_source/t_coffee\r
@@ -64,7 +66,7 @@ probcons.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
 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/jronn3.1.jar\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
@@ -88,12 +90,25 @@ cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/Glob
 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
-aacon.jar.file=binaries/aaconservation.jar\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