-probcons.limits.file=conf/settings/ProbconsLimits.xml\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=/sw/java/latest/bin/java\r
-cluster.jronn.bin=/sw/java/latest/bin/java\r
-jronn.jar.file=binaries/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 h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00\r
-\r
-\r
-### Disembl configuration - NOT DISTRIBUTED ### \r
-#local.disembl.bin.windows= \r
-local.disembl.bin=/homes/pvtroshin/soft/DisEMBL-1.4raw/DisEMBL.py\r
-cluster.disembl.bin=/homes/pvtroshin/soft/DisEMBL-1.4raw/DisEMBL.py\r
-#disembl.parameters.file=conf/settings/JronnParameters.xml\r
-disembl.limits.file=conf/settings/JronnLimits.xml\r
-disembl.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+#probcons.limits.file=conf/settings/ProbconsLimits.xml\r
+#probcons.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+\r
+\r
+##### JRONN CONFIGURATION ######\r
+## If no local path is specified, Java is loaded from JAVA_HOME environment \r
+## variable for local execution. However, cluster.jronn.bin must be specified for \r
+## running Jronn on the cluster. \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.limits.file=conf/settings/JronnLimits.xml\r
+## Jronn can use multiple CPUs\r
+## This parameter specifies the number of CPU to use\r
+#jronn.cluster.cpunum=4\r
+## This reserves a slot with CPUNUM on the cluster for the task\r
+#jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00\r
+\r
+\r
+##### DISEMBL CONFIGURATION ###### \r
+local.disembl.bin=binaries/src/disembl/DisEMBL.py\r
+#cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py\r
+#disembl.limits.file=conf/settings/DisemblLimits.xml\r
+#disembl.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+\r
+\r
+##### GLOBPLOT CONFIGURATION ###### \r
+local.globplot.bin=binaries/src/globplot/GlobPlot.py\r
+#cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/GlobPlot.py\r
+#globplot.bin.env=PYTHONPATH#/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/biopython-1.50 \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
+\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 \r
+## depends on. This path will be converted to absolute if relative at runtime. \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
+\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 can use multiple CPUs\r
+## This parameter specifies the number of CPUs to use\r
+#aacon.cluster.cpunum=4\r
+## This reserves a slot with CPUNUM on the cluster for the task\r
+#aacon.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00\r