JWS-71 - nominal Limits for RNAFold service - necessary so 'drmaa

library not found' exception isn't raised when submitting to cluster

diff --git a/conf/Executable.properties b/conf/Executable.properties
index ba9b4a7..28b9f66 100644 (file)
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -199,5 +199,9 @@ aacon.presets.file=conf/settings/AAConPresets.xml
 #####                                  RNAALIFOLD CONFIGURATION                         ######\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/RNAalifoldOptionsOnly.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

diff --git a/conf/settings/RNAalifoldLimits.xml b/conf/settings/RNAalifoldLimits.xml
new file mode 100644 (file)
index 0000000..381962e
--- /dev/null
+++ b/conf/settings/RNAalifoldLimits.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
+<limits>
+ <runnerClassName>compbio.runner.structure.RNAaliFold</runnerClassName>
+  <limit isDefault="true">
+    <seqNumber>1000</seqNumber>
+    <seqLength>1000</seqLength>
+  </limit>
+  <limit isDefault="false">
+    <preset># LocalEngineExecutionLimit #</preset>
+    <seqNumber>100</seqNumber>
+    <seqLength>200</seqLength>
+  </limit>
+</limits>