JWS-113 Commented Jpred entries in various configuration files.

diff --git a/WEB-INF/sun-jaxws.xml b/WEB-INF/sun-jaxws.xml
index 13d6fac..eff3279 100644 (file)
--- a/WEB-INF/sun-jaxws.xml
+++ b/WEB-INF/sun-jaxws.xml
@@ -42,9 +42,9 @@
        <endpoint name='IUPredWS'\r
                implementation='compbio.ws.server.IUPredWS'\r
                url-pattern='/IUPredWS'/>\r
-       <endpoint name='JpredWS'\r
-               implementation='compbio.ws.server.JpredWS'\r
-               url-pattern='/JpredWS'/>\r
+       <!--<endpoint name='JpredWS'-->\r
+               <!--implementation='compbio.ws.server.JpredWS'-->\r
+               <!--url-pattern='/JpredWS'/>-->\r
        <endpoint name='RNAalifoldWS'\r
                implementation='compbio.ws.server.RNAalifoldWS'\r
                url-pattern='/RNAalifoldWS'/>\r

diff --git a/WEB-INF/web.xml b/WEB-INF/web.xml
index cec1884..6ec75a1 100644 (file)
--- a/WEB-INF/web.xml
+++ b/WEB-INF/web.xml
@@ -174,11 +174,11 @@
                <load-on-startup>1</load-on-startup>\r
        </servlet>\r
 \r
-       <servlet>\r
-               <servlet-name>JpredWS</servlet-name>\r
-               <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
-               <load-on-startup>1</load-on-startup>\r
-       </servlet>\r
+       <!--<servlet>-->\r
+               <!--<servlet-name>JpredWS</servlet-name>-->\r
+               <!--<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>-->\r
+               <!--<load-on-startup>1</load-on-startup>-->\r
+       <!--</servlet>-->\r
        <servlet>\r
                <servlet-name>RNAalifoldWS</servlet-name>\r
                <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
@@ -296,10 +296,10 @@
                <url-pattern>/IUPredWS</url-pattern>\r
        </servlet-mapping>\r
 \r
-       <servlet-mapping>\r
-               <servlet-name>JpredWS</servlet-name>\r
-               <url-pattern>/JpredWS</url-pattern>\r
-       </servlet-mapping>\r
+       <!--<servlet-mapping>-->\r
+               <!--<servlet-name>JpredWS</servlet-name>-->\r
+               <!--<url-pattern>/JpredWS</url-pattern>-->\r
+       <!--</servlet-mapping>-->\r
 \r
        <servlet-mapping>\r
                <servlet-name>RNAalifoldWS</servlet-name>\r

diff --git a/binaries/src/setexecflag.sh b/binaries/src/setexecflag.sh
index 38ad0fa..7e300ed 100644 (file)
--- a/binaries/src/setexecflag.sh
+++ b/binaries/src/setexecflag.sh
@@ -32,8 +32,8 @@ chmod +x globplot/GlobPlot.py globplot/sav_gol
 echo "Setting executable flag for IUPred..."
 chmod +x iupred/iupred
 
-echo "Setting executable flag for Jpred..."
-chmod +x jpred/i686/* jpred/x86_64/*
+#echo "Setting executable flag for Jpred..."
+#chmod +x jpred/i686/* jpred/x86_64/*
 
 echo "Setting executable flag for ViennaRNA..."
 chmod +x ViennaRNA/Progs/RNAalifold

diff --git a/conf/Executable.properties b/conf/Executable.properties
index cbc8474..cfacc2f 100644 (file)
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -215,22 +215,22 @@ aacon.limits.file        = conf/settings/AAConLimits.xml
 ###########################################################################################\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\r
-# The varible jpred.data.uniref.path define a path to Uniref90 files used by Jpred. If \r
-# you install the database to a different path chenge the variable here\r
-jpred.data.uniref.path = /data/UNIREFdb\r
-# WARNING!!! \r
-# Redefine jpred.data.uniref.name if you do undestand what the variable means\r
-jpred.data.uniref.name = cluster\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
+#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\r
+## The varible jpred.data.uniref.path define a path to Uniref90 files used by Jpred. If\r
+## you install the database to a different path chenge the variable here\r
+#jpred.data.uniref.path = /data/UNIREFdb\r
+## WARNING!!!\r
+## Redefine jpred.data.uniref.name if you do undestand what the variable means\r
+#jpred.data.uniref.name = cluster\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

diff --git a/wsbuild.xml b/wsbuild.xml
index c8aa0e5..c6966f6 100644 (file)
--- a/wsbuild.xml
+++ b/wsbuild.xml
@@ -18,7 +18,7 @@
        </path>\r
 \r
        <property name="wsdl.dir" location="${basedir}/webservices/compbio/ws/server/resource" />\r
-       <property name="jpred.wsdl" location="${wsdl.dir}/JpredWS.wsdl" />\r
+       <!--<property name="jpred.wsdl" location="${wsdl.dir}/JpredWS.wsdl" />-->\r
        <property name="aacon.wsdl" location="${wsdl.dir}/AAConWS.wsdl" />\r
        <property name="clustal.wsdl" location="${wsdl.dir}/ClustalWS.wsdl" />\r
        <property name="muscle.wsdl" location="${wsdl.dir}/MuscleWS.wsdl" />\r
@@ -56,18 +56,18 @@
                <!-- destdir - Where to put generated classes -->\r
                <!-- sourcedestdir -  Where to put generated source files -->\r
                <!-- resourcedestdir - Where to put generated source files -->\r
-               <wsgen sei="compbio.ws.server.JpredWS"\r
-                               sourcedestdir="${basedir}/webservices"\r
-                               destdir="${classes}"\r
-                               resourcedestdir="${wsdl.dir}"\r
-                               keep="true"\r
-                               genwsdl="true"\r
-                               extension="false"\r
-                               xendorsed="true"\r
-                               verbose="true">\r
-                               <classpath refid="classes.path" />\r
-                               <classpath refid="project.classpath" />\r
-               </wsgen>\r
+               <!--<wsgen sei="compbio.ws.server.JpredWS"-->\r
+                               <!--sourcedestdir="${basedir}/webservices"-->\r
+                               <!--destdir="${classes}"-->\r
+                               <!--resourcedestdir="${wsdl.dir}"-->\r
+                               <!--keep="true"-->\r
+                               <!--genwsdl="true"-->\r
+                               <!--extension="false"-->\r
+                               <!--xendorsed="true"-->\r
+                               <!--verbose="true">-->\r
+                               <!--<classpath refid="classes.path" />-->\r
+                               <!--<classpath refid="project.classpath" />-->\r
+               <!--</wsgen>-->\r
                <wsgen sei="compbio.ws.server.AAConWS"\r
                                sourcedestdir="${basedir}/webservices"\r
                                destdir="${classes}"\r