\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
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
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_14\\bin\\java.exe \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/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
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
+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
-local.aacon.bin.windows=D:\\Java\\jdk1.6.0_14\\bin\\java.exe \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