Linux Release

build.xml

@@ -379,14 +379,20 @@ Here are the targets that count:
 		<copy todir="${app.linExeDir}/BioFabric/lib/lin-jre-${app.jdkVer}">
 			<fileset dir="${app.JREDir}/lin-jre-${app.jdkVer}" />
 		</copy>
+		<!--Dang ant copy loses the permissions -->
+		<chmod file="${app.linExeDir}/BioFabric/BioFabric${app.macDiskVersion}.sh" perm="+x"/>
+		<chmod file="${app.linExeDir}/BioFabric/lib/lin-jre-${app.jdkVer}/bin/java" perm="+x"/>
+		<chmod file="${app.linExeDir}/BioFabric/lib/lin-jre-${app.jdkVer}/bin/keytool" perm="+x"/>
 		<copy file="${app.signDir}/${app.signJarFile}" tofile="${app.linExeDir}/BioFabric/lib/${app.signJarFile}" />
 		<exec executable="/usr/bin/find" failonerror="true">
 			<arg line="${app.linExeDir}/BioFabric -name .DS_Store -delete"/>
-		</exec>	
-		<tar destfile="${app.linuxDistFile}" 
-			 basedir="${app.linExeDir}/BioFabric"
-			 compression="gzip">
-		</tar>
+		</exec>
+		<!--Dang ant tar loses the permissions too-->
+	    <exec executable="/usr/bin/tar" failonerror="true" dir="${app.linExeDir}">
+	        <arg value="-cvzf"/>
+	        <arg value="${app.linuxDistFile}"/>
+	        <arg value="BioFabric"/>
+	    </exec>
 		<exec executable="/sbin/md5" failonerror="true" output="${app.linuxDistFile}-MD5.txt">
 			<arg line="${app.linuxDistFile}" />
 		</exec>

executables/Linux/BioFabricTemplate.sh

@@ -2,5 +2,5 @@
 
 JARPATH=`dirname $0`
 JAVA_HOME=${JARPATH}/lib/__WJRL_JDK_VER__
-$JAVA_HOME/bin/java -Xmx8000m -classpath ${JARPATH}/lib/sBioFabric-__WJRL_VERNUM__.jar org.systemsbiology.biofabric.app.BioFabricApplication $*
+$JAVA_HOME/bin/java -Xmx8000m -jar ${JARPATH}/lib/sBioFabric-V__WJRL_VERNUM__.jar org.systemsbiology.biofabric.app.BioFabricApplication $*
 

releaseDistArchive/BioFabric-2.0.B.2.tgz-MD5.txt

@@ -0,0 +1 @@
+MD5 (BioFabric-2.0.B.2.tgz) = 28257bec3932165a6902d59964f40278

releaseTools/makeJREs.sh

@@ -27,8 +27,8 @@ cd ${JRE_TARG}
 if [ ${WHICH} = "Linux" ]; then
   rm -rf lin-jre-${JDK_VER}
 
-  ${MAC_JAVA_HOME}/bin/jlink --module-path ${WIN_JAVA_HOME}/jmods --add-modules ${JRE_DEPS} --output lin-jre-${JDK_VER} --strip-debug --compress 2 --no-header-files --no-man-pages
-
+  ${MAC_JAVA_HOME}/bin/jlink --module-path ${LIN_JAVA_HOME}/jmods --add-modules ${JRE_DEPS} --output lin-jre-${JDK_VER} --strip-debug --compress 2 --no-header-files --no-man-pages
+  chmod +x lin-jre-${JDK_VER}/bin/*
   find lin-jre-${JDK_VER} -name .DS_Store -delete
 fi