X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=conf%2FExecutable.properties;h=b9bdac3bf7acb43fe584a1847c2d03baf9e69fa3;hb=2c1c5633a7d1c31008e04136cc4dae6fca1b369e;hp=247c9f50950b54176c5663abafb7b1cf96379096;hpb=fab6bab770b548a0c99ed6f5dfb46f5aa99f67c7;p=jabaws.git

diff --git a/conf/Executable.properties b/conf/Executable.properties
index 247c9f5..b9bdac3 100644
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -1,6 +1,6 @@
 
 ### Clustal configuration ###
-local.clustalw.bin.windows=binaries/clustalw2.exe
+local.clustalw.bin.windows=binaries/windows/clustalw2.exe
 local.clustalw.bin=binaries/src/clustalw/src/clustalw2
 cluster.clustalw.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalw/src/clustalw2
 # Parameters names which come from RunnerConfig -> Parameters.xml file ultimately are all lowercased in comparison!
@@ -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
 
 ### Muscle configuration ###
-local.muscle.bin.windows=binaries/muscle.exe
+local.muscle.bin.windows=binaries/windows/muscle.exe
 local.muscle.bin=binaries/src/muscle/muscle
 # Beware version of muscle on the cluster older and does not support some 
 # of the newer version attributed thus, will not work with Muscle.java wrapper!
@@ -61,30 +61,52 @@ probcons.limits.file=conf/settings/ProbconsLimits.xml
 probcons.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
 
 ### Jronn configuration ### 
-local.jronn.bin.windows=D:\\Java\\jdk1.6.0_14\\bin\\java.exe 
+local.jronn.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe 
 local.jronn.bin=/sw/java/latest/bin/java
 cluster.jronn.bin=/sw/java/latest/bin/java
-jronn.jar.file=binaries/jronn3.1.jar
-jronn.parameters.file=conf/settings/JronnParameters.xml
+jronn.jar.file=binaries/windows/jronn3.1.jar
+# jronn.parameters.file=conf/settings/JronnParameters.xml
 jronn.limits.file=conf/settings/JronnLimits.xml
 #TODO jronn.jvm.options=-Xms32M -Xmx512M
 jronn.cluster.cpunum=4
 jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00
 
 
-### Disembl configuration - NOT DISTRIBUTED ### 
+### Disembl configuration Tisean - Disembl dependancy ### 
 #local.disembl.bin.windows= 
-local.disembl.bin=/homes/pvtroshin/soft/DisEMBL-1.4raw/DisEMBL.py
-cluster.disembl.bin=/homes/pvtroshin/soft/DisEMBL-1.4raw/DisEMBL.py
-#disembl.parameters.file=conf/settings/JronnParameters.xml
+local.disembl.bin=binaries/src/disembl/DisEMBL.py
+cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py
+# disembl.parameters.file=conf/settings/DisemblParameters.xml
 disembl.limits.file=conf/settings/DisemblLimits.xml
 disembl.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
 
-local.aacon.bin.windows=D:\\Java\\jdk1.6.0_14\\bin\\java.exe 
+### GlobPlot configuration Tisean - GlobPlot and Disembl dependancy ### 
+#local.disembl.bin.windows= 
+local.globplot.bin=binaries/src/globplot/GlobPlot.py
+cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/GlobPlot.py
+# globplot.parameters.file=conf/settings/GlobPlotParameters.xml
+globplot.limits.file=conf/settings/GlobPlotLimits.xml
+globplot.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
+
+### IUPred configuration ### 
+local.iupred.bin.windows=binaries/windows/iupred/iupred.exe 
+local.iupred.bin=binaries/src/iupred/iupred
+# This must point to the directory where iupred binary is, with other files it depends on
+iupred.bin.env=IUPred_PATH#/homes/pvtroshin/workspace/jaba2/binaries/src/iupred
+cluster.iupred.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/iupred/iupred
+iupred.parameters.file=conf/settings/IUPredParameters.xml
+iupred.limits.file=conf/settings/IUPredLimits.xml
+iupred.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
+
+### AACon configuration ###
+# This is just a path to the standard java executable 
+local.aacon.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe 
 local.aacon.bin=/sw/java/latest/bin/java
 cluster.aacon.bin=/sw/java/latest/bin/java
-aacon.jar.file=binaries/aaconservation.jar
+# Path to the AACon library
+aacon.jar.file=binaries/windows/aaconservation.jar
 aacon.parameters.file=conf/settings/AAConParameters.xml
+aacon.presets.file=conf/settings/AAConPresets.xml
 aacon.limits.file=conf/settings/AAConLimits.xml
 #TODO jronn.jvm.options=-Xms32M -Xmx512M
 aacon.cluster.cpunum=4