-tcoffee.bin.env=HOME_4_TCOFFEE#jobsout;\r
-tcoffee.presets.file=conf/settings/TcoffeePresets.xml\r
-tcoffee.parameters.file=conf/settings/TcoffeeParameters.xml\r
-tcoffee.limits.file=conf/settings/TcoffeeLimits.xml\r
-tcoffee.cluster.cpunum=4\r
-tcoffee.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00 \r
-\r
-### Probcons configuration ###\r
-#local.probcons.bin.windows=\r
-local.probcons.bin=binaries/src/probcons/probcons\r
-cluster.probcons.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/probcons/probcons\r
-#Probcons does not support matrix loading - unrecognised option reported! \r
-probcons.parameters.file=conf/settings/ProbconsParameters.xml\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
-### 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 h_vmem=1700M -l ram=1700M -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 h_vmem=6000M -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
-#globplot.bin.env=PYTHONHOME#/usr/local/lib/python2.6; \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 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
-# 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 h_vmem=6000M -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
-#TODO jronn.jvm.options=-Xms32M -Xmx512M\r
-aacon.cluster.cpunum=4\r
+tcoffee.bin.env = HOME_4_TCOFFEE#jobsout;\r
+tcoffee.presets.file = conf/settings/TcoffeePresets.xml\r
+tcoffee.parameters.file = conf/settings/TcoffeeParameters.xml\r
+tcoffee.limits.file = conf/settings/TcoffeeLimits.xml\r
+### Tcoffee can be executed on multiple CPUs if run on the cluster. This parameter defines CPUs #N\r
+#tcoffee.cluster.cpunum = 4\r
+### This paramer defines queue setting with CPUNUM on the cluster\r
+#tcoffee.cluster.settings = -q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00\r
+\r
+\r
+###########################################################################################\r
+# PROBCONS CONFIGURATION #\r
+###########################################################################################\r
+local.probcons.bin = binaries/src/probcons/probcons\r
+#cluster.probcons.bin = /home/jabaws/binaries/src/probcons/probcons\r
+probcons.parameters.file = conf/settings/ProbconsParameters.xml\r
+probcons.limits.file = conf/settings/ProbconsLimits.xml\r
+### This parameter defines queue settings for PROBCON on the cluster\r
+#probcons.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M\r
+\r
+\r
+###########################################################################################\r
+# JRONN CONFIGURATION #\r
+###########################################################################################\r
+### If no local path is specified, Java is loaded from JAVA_HOME variable for local \r
+### execution. However, cluster.jronn.bin MUST be specified for 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/bj3.0.4p-jronn.jar\r
+jronn.limits.file = conf/settings/JronnLimits.xml\r
+## Jronn can use multiple CPUs. This parameter specifies the number of CPUs\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_cpu=24:00:00\r
+\r
+\r
+###########################################################################################\r
+# DISEMBL CONFIGURATION #\r
+###########################################################################################\r
+local.disembl.bin = binaries/src/disembl/DisEMBL.py\r
+#cluster.disembl.bin = /home/jabaws/binaries/src/disembl/DisEMBL.py\r
+disembl.limits.file = conf/settings/DisemblLimits.xml\r
+#disembl.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M\r
+\r
+\r
+###########################################################################################\r
+# GLOBPLOT CONFIGURATION #\r
+###########################################################################################\r
+local.globplot.bin = binaries/src/globplot/GlobPlot.py\r
+#cluster.globplot.bin = /home/jabaws/binaries/src/globplot/GlobPlot.py\r
+#globplot.bin.env = PYTHONPATH#/home/jabaws/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 ram=6000M\r
+\r
+\r
+###########################################################################################\r
+# IUPRED CONFIGURATION #\r
+###########################################################################################\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 = /home/jabaws/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
+\r
+###########################################################################################\r
+# AACON CONFIGURATION #\r
+###########################################################################################\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. This parameter defines the number of CPUs:\r
+#aacon.cluster.cpunum = 4\r
+### This parameter defines queue settings for AACON on the cluster\r
+#aacon.cluster.settings = -q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00\r
+\r
+###########################################################################################\r
+# JPRED CONFIGURATION #\r
+###########################################################################################\r
+local.jpred.bin = binaries/src/jpred/jpred.pl\r
+#cluster.jpred.bin = /home/jabaws/binaries/src/jpred/jpred.pl\r
+# These paths will be converted to absolute if relative.\r
+jpred.bin.env = BLASTMAT#binaries/src/jpred/data/blast;UNIREFDB#binaries/src/jpred/unirefdb;\r
+### This parameters specifies the directory where the matrices files are stored\r
+jpred.presets.file = conf/settings/JpredPresets.xml\r
+jpred.parameters.file = conf/settings/JpredParameters.xml\r
+jpred.limits.file = conf/settings/JpredLimits.xml\r
+jpred.cluster.cpunum = 4\r
+#jpred.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M\r
+\r
+###########################################################################################\r
+# RNAALIFOLD CONFIGURATION #\r
+###########################################################################################\r
+local.rnaalifold.bin.windows = binaries/windows/ViennaRNA/RNAalifold.exe\r
+local.rnaalifold.bin = binaries/src/ViennaRNA/Progs/RNAalifold\r
+#cluster.rnaalifold.bin = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/ViennaRNA/Progs/RNAalifold\r
+rnaalifold.parameters.file = conf/settings/RNAalifoldParameters.xml\r
+rnaalifold.limits.file = conf/settings/RNAalifoldLimits.xml\r
+rnaalifold.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M\r
+\r
+\r