Added scripts into Mac .app files to allow running from command line.…

… Incremented release number in pom.
sanger-pathogens · Jan 17, 2019 · 1708b25 · 1708b25
1 parent 2fc4340
commit 1708b25
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Showing 7 changed files with 66 additions and 11 deletions.
diff --git a/act b/act
@@ -97,6 +97,7 @@ done
 JAR_NAME=act.jar
 JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
 JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
+ARTEMIS_CP=$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED
 
 #
 # Use a custom Java version if necessary
@@ -135,14 +136,16 @@ PLATTMP=`uname`
 if [[ "$PLATTMP" = "Darwin" ]]
 then
   	APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dapple.laf.useScreenMenuBar=true -Xdock:name=ACT"
+  	JAR_FILE_MACAPP=$APPLICATION_HOME/Java/$JAR_NAME
+  	ARTEMIS_CP="$JAR_FILE_MACAPP:$ARTEMIS_CP"
 fi
 
 if [[ "$QUIET" = no ]]
 then
     echo "Starting ACT with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
 fi
 
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.ActMain $*
+$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.components.ActMain $*
 result=$?
 
 exit $result

diff --git a/art b/art
@@ -103,6 +103,7 @@ done
 JAR_NAME=artemis.jar
 JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
 JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
+ARTEMIS_CP=$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED
 
 #
 # Use a custom Java version if necessary
@@ -142,14 +143,16 @@ PLATTMP=`uname`
 if [[ "$PLATTMP" = "Darwin" ]]
 then
   	APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dapple.laf.useScreenMenuBar=true -Xdock:name=Artemis"
+  	JAR_FILE_MACAPP=$APPLICATION_HOME/Java/$JAR_NAME
+  	ARTEMIS_CP="$JAR_FILE_MACAPP:$ARTEMIS_CP"
 fi
 
 if [[ "$QUIET" = "no" ]]
 then
     echo "Starting Artemis with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
 fi
 
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.ArtemisMain $*
+$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.components.ArtemisMain $*
 result=$?
 
 exit $result

diff --git a/bamview b/bamview
@@ -40,6 +40,7 @@ APPLICATION_PROPERTIES="-Djdbc.drivers=org.postgresql.Driver -Dartemis.environme
 JAR_NAME=bamview.jar
 JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
 JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
+ARTEMIS_CP=$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED
 
 #
 # Use a custom Java version if necessary
@@ -72,14 +73,16 @@ PLATTMP=`uname`
 if [[ "$PLATTMP" = "Darwin" ]]
 then
   	APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Xdock:name=BamView"
+  	JAR_FILE_MACAPP=$APPLICATION_HOME/Java/$JAR_NAME
+  	ARTEMIS_CP="$JAR_FILE_MACAPP:$ARTEMIS_CP"
 fi
 
 if [[ "$QUIET" = "no" ]]
 then
     echo "Starting BamView with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
 fi
 
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.alignment.BamView $*
+$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.components.alignment.BamView $*
 result=$?
 
 exit $result
diff --git a/dnaplotter b/dnaplotter
@@ -79,6 +79,7 @@ done
 JAR_NAME=dnaplotter.jar
 JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
 JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
+ARTEMIS_CP=$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED
 
 #
 # Use a custom Java version if necessary
@@ -111,14 +112,16 @@ PLATTMP=`uname`
 if [[ "$PLATTMP" = "Darwin" ]]
 then
   	APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dapple.laf.useScreenMenuBar=true -Xdock:name=Circular-Plot"
+  	JAR_FILE_MACAPP=$APPLICATION_HOME/Java/$JAR_NAME
+  	ARTEMIS_CP="$JAR_FILE_MACAPP:$ARTEMIS_CP"
 fi
 
 if [[ "$QUIET" = "no" ]]
 then
     echo "Starting DNA Plotter with arguments: $FLAGS $APPLICATION_PROPERTIES $TEMPLATE_FILE_ARG"
 fi
 
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.circular.DNADraw $TEMPLATE_FILE_ARG
+$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.circular.DNADraw $TEMPLATE_FILE_ARG
 result=$?
 
 exit $result

diff --git a/etc/versions b/etc/versions
@@ -1,4 +1,4 @@
-Artemis Release 18.0.0
-ACT Release 18.0.0
-DNAPlotter Release 18.0.0
-BamView 18.0.0
+Artemis Release 18.0.1
+ACT Release 18.0.1
+DNAPlotter Release 18.0.1
+BamView 18.0.1
diff --git a/pom.xml b/pom.xml
@@ -5,7 +5,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>uk.ac.sanger</groupId>
 	<artifactId>artemis</artifactId>
-	<version>18.0.0</version>
+	<version>18.0.1</version>
 
 	<name>Artemis</name>
 	<description>Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.
@@ -93,8 +93,7 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
 
         <!-- Java version-->
         <java.compatibility.major.version>9</java.compatibility.major.version>
-
-		<bundler.jdk.path>/Library/Java/JavaVirtualMachines/jdk-10.0.2.jdk</bundler.jdk.path>
+
 		<osx.bundler.jar>${project.basedir}/maven-lib/appbundler-1.0ea.jar</osx.bundler.jar>
 		<osx.bundler.volume>Artemis_Tools</osx.bundler.volume>
 		<osx.bundler.chado.volume>Artemis_Tools_Chado</osx.bundler.chado.volume>

diff --git a/src/assembly/macosx-release-assembly.xml b/src/assembly/macosx-release-assembly.xml
@@ -152,6 +152,28 @@
 		<fileset dir="etc"/>
 	</copy>
 
+	<!-- Copy in scripts for use on command line -->
+	<copy todir="${osx.app.folder}/apps/${artemis.application.name}.app/Contents/">
+		<fileset file="art"/>
+	</copy>
+	<copy todir="${osx.app.folder}/apps/${act.application.name}.app/Contents/">
+		<fileset file="act"/>
+	</copy>
+	<copy todir="${osx.app.folder}/apps/${dnaplotter.application.name}.app/Contents/">
+		<fileset file="dnaplotter"/>
+	</copy>
+	<copy todir="${osx.app.folder}/apps/${bamview.application.name}.app/Contents/">
+		<fileset file="bamview"/>
+	</copy>
+
+	<!-- Set script permission -->
+	<chmod perm="a+x">
+		<fileset file="${osx.app.folder}/apps/${artemis.application.name}.app/Contents/art"/>
+		<fileset file="${osx.app.folder}/apps/${act.application.name}.app/Contents/act"/>
+		<fileset file="${osx.app.folder}/apps/${dnaplotter.application.name}.app/Contents/dnaplotter"/>
+		<fileset file="${osx.app.folder}/apps/${bamview.application.name}.app/Contents/bamview"/>
+	</chmod>
+
 	<echo>NOTE: hdiutil must be installed to create a Mac .dmg image file...</echo>
 
 	<exec executable="hdiutil">
@@ -305,6 +327,28 @@
 		<fileset dir="etc"/>
 	</copy>
 
+	<!-- Copy in scripts for use on command line -->
+	<copy todir="${osx.app.chado.folder}/apps/${artemis.chado.application.name}.app/Contents/">
+		<fileset file="art"/>
+	</copy>
+	<copy todir="${osx.app.chado.folder}/apps/${act.chado.application.name}.app/Contents/">
+		<fileset file="act"/>
+	</copy>
+	<copy todir="${osx.app.chado.folder}/apps/${dnaplotter.application.name}.app/Contents/">
+		<fileset file="dnaplotter"/>
+	</copy>
+	<copy todir="${osx.app.chado.folder}/apps/${bamview.application.name}.app/Contents/">
+		<fileset file="bamview"/>
+	</copy>
+
+	<!-- Set script permission -->
+	<chmod perm="a+x">
+		<fileset file="${osx.app.chado.folder}/apps/${artemis.chado.application.name}.app/Contents/art"/>
+		<fileset file="${osx.app.chado.folder}/apps/${act.chado.application.name}.app/Contents/act"/>
+		<fileset file="${osx.app.chado.folder}/apps/${dnaplotter.application.name}.app/Contents/dnaplotter"/>
+		<fileset file="${osx.app.chado.folder}/apps/${bamview.application.name}.app/Contents/bamview"/>
+	</chmod>
+
 	<echo>NOTE: hdiutil must be installed to create a Mac .dmg image file...</echo>
 
 	<exec executable="hdiutil">