X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=conf%2FExecutable.properties;h=caf735577f5f0c78f7855b884cb5bdfcad603ce7;hb=550d715f5af9271247b20363d1212e7e0279f9ee;hp=1562c56bd6d0f2a4fd64712f3c4d323b48fa14c5;hpb=d3806a66f002b93f6dc03447b6628f943a3ba90c;p=jabaws.git

diff --git a/conf/Executable.properties b/conf/Executable.properties
index 1562c56..caf7355 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!
@@ -28,8 +28,9 @@ muscle.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
 
 ### Mafft configuration ###
 #local.mafft.bin.windows=
-local.mafft.bin=binaries/src/mafft/binaries/mafft
-cluster.mafft.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/mafft/core/mafft
+local.mafft.bin=binaries/src/mafft/scripts/mafft
+cluster.mafft.bin=/homes/pvtroshin/workspace/jaba2/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;
 mafft.--aamatrix.path=binaries/matrices
 mafft.presets.file=conf/settings/MafftPresets.xml
@@ -37,6 +38,7 @@ mafft.parameters.file=conf/settings/MafftParameters.xml
 mafft.limits.file=conf/settings/MafftLimits.xml
 mafft.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
 
+
 ### Tcoffee configuration ###
 local.tcoffee.bin=binaries/src/tcoffee/t_coffee_source/t_coffee
 cluster.tcoffee.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/tcoffee/t_coffee_source/t_coffee
@@ -61,11 +63,11 @@ 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
@@ -76,7 +78,7 @@ jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l
 #local.disembl.bin.windows= 
 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.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
 
@@ -84,16 +86,31 @@ disembl.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
 #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
+# Dundee only settings
+globplot.bin.env=PYTHONPATH#/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/biopython-1.50 
+# 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
+# This path will be converted to absolute if relative. 
+iupred.bin.env=IUPred_PATH#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 ###
-local.aacon.bin.windows=D:\\Java\\jdk1.6.0_14\\bin\\java.exe 
+# 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