+probcons.cluster.settings=-l h_cpu=24:00:00 -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 ram=6000M -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 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 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 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
+aacon.cluster.cpunum=4\r
+aacon.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=6000M -l h_cpu=24:00:00\r