From 16ac5f3ad57574a37aa7e013813c4f0b33b87508 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 30 Aug 2013 15:53:59 +0100
Subject: [PATCH] JWS-71 - nominal Limits for RNAFold service - necessary so
 'drmaa library not found' exception isn't raised when
 submitting to cluster

---
 conf/Executable.properties         |    4 ++++
 conf/settings/RNAalifoldLimits.xml |   13 +++++++++++++
 2 files changed, 17 insertions(+)
 create mode 100644 conf/settings/RNAalifoldLimits.xml

diff --git a/conf/Executable.properties b/conf/Executable.properties
index ba9b4a7..28b9f66 100644
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -199,5 +199,9 @@ aacon.presets.file=conf/settings/AAConPresets.xml
 #####					RNAALIFOLD CONFIGURATION			 ######
 local.rnaalifold.bin.windows=binaries/windows/ViennaRNA/RNAalifold.exe
 local.rnaalifold.bin=binaries/src/ViennaRNA/Progs/RNAalifold
+#cluster.rnaalifold.bin=/homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/ViennaRNA/Progs/RNAalifold
 rnaalifold.parameters.file=conf/settings/RNAalifoldOptionsOnly.xml
+rnaalifold.limits.file=conf/settings/RNAalifoldLimits.xml
+rnaalifold.cluster.settings=-P webservices -R y -l h_cpu=24:00:00 -l ram=6000M
+
 
diff --git a/conf/settings/RNAalifoldLimits.xml b/conf/settings/RNAalifoldLimits.xml
new file mode 100644
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>
-- 
1.7.10.2