From: Fábio Madeira <fmmarquesmadeira@dundee.ac.uk>
Date: Wed, 8 Feb 2017 10:19:08 +0000 (+0000)
Subject: JWS-114 Added a missing section to Executable.properties.dundee (from Executable... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c3be052f4089b37e5ccb9e4c40204bfb0f07af52;p=jabaws.git

JWS-114 Added a missing section to Executable.properties.dundee (from Executable.properties).
---

diff --git a/conf/Executable.properties.dundee b/conf/Executable.properties.dundee
index 8d5c761..fce1b21 100644
--- a/conf/Executable.properties.dundee
+++ b/conf/Executable.properties.dundee
@@ -210,3 +210,51 @@ aacon.limits.file        = conf/settings/AAConLimits.xml
 aacon.cluster.cpunum     = 4
 ### This reserves a slot with CPUNUM on the cluster for the task
 aacon.cluster.settings   = -P webservices -R y -q 64bit-pri.q -pe smp 4 -l ram=3400M -l h_cpu=24:00:00
+
+###########################################################################################
+#                               JPRED CONFIGURATION                                       #
+###########################################################################################
+#local.jpred.bin        = binaries/src/jpred/jpred.pl
+##cluster.jpred.bin      = /home/jabaws/binaries/src/jpred/jpred.pl
+## These paths will be converted to absolute if relative.
+#jpred.bin.env          = BLASTMAT#binaries/src/jpred/data/blast
+## The varible jpred.data.uniref.path define a path to Uniref90 files used by Jpred. If
+## you install the database to a different path chenge the variable here
+#jpred.data.uniref.path = /data/UNIREFdb
+## WARNING!!!
+## Redefine jpred.data.uniref.name if you do undestand what the variable means
+#jpred.data.uniref.name = cluster
+#### This parameters specifies the directory where the matrices files are stored
+#jpred.presets.file     = conf/settings/JpredPresets.xml
+#jpred.parameters.file  = conf/settings/JpredParameters.xml
+#jpred.limits.file      = conf/settings/JpredLimits.xml
+#jpred.cluster.cpunum   = 4
+##jpred.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M
+
+###########################################################################################
+#                               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/RNAalifoldParameters.xml
+rnaalifold.limits.file       = conf/settings/RNAalifoldLimits.xml
+rnaalifold.cluster.settings  = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M
+
+###########################################################################################
+#                                 MSAProbs CONFIGURATION                                  #
+###########################################################################################
+local.msaprobs.bin         = binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs
+cluster.msaprobs.bin       = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs
+msaprobs.parameters.file   = conf/settings/MSAprobsParameters.xml
+msaprobs.limits.file       = conf/settings/MSAprobsLimits.xml
+msaprobs.cluster.settings  = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M
+
+###########################################################################################
+#                                  GLprobs CONFIGURATION                                  #
+###########################################################################################
+local.glprobs.bin         = binaries/src/GLProbs-1.0/glprobs
+cluster.glprobs.bin       = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/GLProbs-1.0/glprobs
+glprobs.parameters.file   = conf/settings/GLprobsParameters.xml
+glprobs.limits.file       = conf/settings/GLprobsLimits.xml
+glprobs.cluster.settings  = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M