Packages/prepare/artemis/fix_bin.patch

Description: Simplifying the provided launchers
 Many options or tricks are useless on a Debian system.
 The paths are also adapted to the Debian install.
Author: Pierre Gruet <pgt@debian.org>
Forwarded: not-needed
Last-Update: 2020-09-06

--- a/act
+++ b/act
@@ -38,36 +38,6 @@
     exit 0
 }
 
-add_proxy_properties() {
-
-	if [[ "$http_proxy" = "" ]]
-	then
-		http_proxy=$HTTP_PROXY
-	fi
-	
-	if [[ "$http_proxy" = "" ]]
-	then
-	 	http_proxy=$HTTP_proxy
-	fi
-	
-	if [[ "$http_proxy" != "" ]]
-	then
-		APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
-	fi
-}
-
-#
-# Resolve script path (inc symlinks)
-#
-SOURCE="${BASH_SOURCE[0]}"
-while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
-    DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
-    SOURCE="$(readlink "$SOURCE")"
-    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
-done
-APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script
-
-
 # Special Sanger override on chado PGUSER
 if [[ "$ARTEMIS_SANGER_DBUSER" != "" ]]
 then
@@ -93,28 +63,6 @@
     shift
 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:$JAR_FILE_INSTALLED
-
-#
-# Use a custom Java version if necessary
-#
-if [[ "$ARTEMIS_JAVA_JRE" = "" ]]
-then
-	JAVA=`which java`
-else
-	JAVA_HOME=$ARTEMIS_JAVA_JRE
-	JAVA=$ARTEMIS_JAVA_JRE/bin/java
-fi
-
-#
-# Allow URLs to work from behind firewalls.
-#
-add_proxy_properties
-
 #
 # "-mx2g" sets the maximum amount of memory to use. 
 # This may need to be increased when dealing with large files
@@ -132,20 +80,12 @@
 #
 FLAGS="$FLAGS --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED"
 
-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 $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.components.ActMain $*
+java $FLAGS $APPLICATION_PROPERTIES -jar /usr/share/artemis/act.jar $*
 result=$?
 
 exit $result
--- a/art
+++ b/art
@@ -44,36 +44,6 @@
     exit 0
 }
 
-add_proxy_properties() {
-
-	if [[ "$http_proxy" = "" ]]
-	then
-		http_proxy=$HTTP_PROXY
-	fi
-	
-	if [[ "$http_proxy" = "" ]]
-	then
-	 	http_proxy=$HTTP_proxy
-	fi
-	
-	if [[ "$http_proxy" != "" ]]
-	then
-		APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
-	fi
-}
-
-#
-# Resolve script path (inc symlinks)
-#
-SOURCE="${BASH_SOURCE[0]}"
-while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
-    DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
-    SOURCE="$(readlink "$SOURCE")"
-    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
-done
-APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script
-
-
 # Special Sanger override on chado PGUSER
 if [[ "$ARTEMIS_SANGER_DBUSER" != "" ]]
 then
@@ -99,28 +69,6 @@
     shift
 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:$JAR_FILE_INSTALLED
-
-#
-# Use a custom Java version if necessary
-#
-if [[ "$ARTEMIS_JAVA_JRE" = "" ]]
-then
-	JAVA=`which java`
-else
-	JAVA_HOME=$ARTEMIS_JAVA_JRE
-	JAVA=$ARTEMIS_JAVA_JRE/bin/java
-fi
-
-#
-# Allow URLs to work from behind firewalls.
-#
-add_proxy_properties
-
 #
 # "-mx2g" sets the maximum amount of memory to use. 
 # This may need to be increased when dealing with large files
@@ -139,20 +87,12 @@
 #
 FLAGS="$FLAGS --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED"
 
-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 $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.components.ArtemisMain $*
+java $FLAGS $APPLICATION_PROPERTIES -jar /usr/share/artemis/artemis.jar $*
 result=$?
 
 exit $result
--- a/bamview
+++ b/bamview
@@ -6,57 +6,7 @@
 
 QUIET=no
 
-add_proxy_properties() {
-
-	if [[ "$http_proxy" = "" ]]
-	then
-		http_proxy=$HTTP_PROXY
-	fi
-	
-	if [[ "$http_proxy" = "" ]]
-	then
-	 	http_proxy=$HTTP_proxy
-	fi
-	
-	if [[ "$http_proxy" != "" ]]
-	then
-		APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
-	fi
-}
-
-#
-# Resolve script path (inc symlinks)
-#
-SOURCE="${BASH_SOURCE[0]}"
-while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
-    DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
-    SOURCE="$(readlink "$SOURCE")"
-    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
-done
-APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script
-
-
 APPLICATION_PROPERTIES="-Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX $SANGER_ARTEMIS_OPTIONS"
-JAR_NAME=bamview.jar
-JAR_FILE_DEFAULT=$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
-#
-if [[ "$ARTEMIS_JAVA_JRE" = "" ]]
-then
-	JAVA=`which java`
-else
-	JAVA_HOME=$ARTEMIS_JAVA_JRE
-	JAVA=$ARTEMIS_JAVA_JRE/bin/java
-fi
-
-#
-# Allow URLs to work from behind firewalls.
-#
-add_proxy_properties
 
 #
 # "-mx2g" sets the maximum amount of memory to use. 
@@ -69,20 +19,12 @@
     FLAGS="$ARTEMIS_JVM_FLAGS -noverify"
 fi
 
-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 $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.components.alignment.BamView $*
+java $FLAGS $APPLICATION_PROPERTIES -jar /usr/share/artemis/bamview.jar $*
 result=$?
 
 exit $result
--- a/dnaplotter
+++ b/dnaplotter
@@ -25,37 +25,6 @@
     exit 0
 }
 
-add_proxy_properties() {
-
-	if [[ "$http_proxy" = "" ]]
-	then
-		http_proxy=$HTTP_PROXY
-	fi
-	
-	if [[ "$http_proxy" = "" ]]
-	then
-	 	http_proxy=$HTTP_proxy
-	fi
-	
-	if [[ "$http_proxy" != "" ]]
-	then
-		APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
-	fi
-}
-
-
-#
-# Resolve script path (inc symlinks)
-#
-SOURCE="${BASH_SOURCE[0]}"
-while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
-    DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
-    SOURCE="$(readlink "$SOURCE")"
-    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
-done
-APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script
-
-
 #
 # Parse arguments.
 #
@@ -75,28 +44,6 @@
     shift
 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:$JAR_FILE_INSTALLED
-
-#
-# Use a custom Java version if necessary
-#
-if [[ "$ARTEMIS_JAVA_JRE" = "" ]]
-then
-	JAVA=`which java`
-else
-	JAVA_HOME=$ARTEMIS_JAVA_JRE
-	JAVA=$ARTEMIS_JAVA_JRE/bin/java
-fi
-
-#
-# Allow URLs to work from behind firewalls.
-#
-add_proxy_properties
-
 #
 # "-mx2g" sets the maximum amount of memory to use. 
 # This may need to be increased when dealing with large files
@@ -108,20 +55,12 @@
     FLAGS="$ARTEMIS_JVM_FLAGS -noverify"
 fi
 
-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 $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.circular.DNADraw $TEMPLATE_FILE_ARG
+java $FLAGS $APPLICATION_PROPERTIES -jar /usr/share/artemis/dnaplotter.jar $TEMPLATE_FILE_ARG
 result=$?
 
 exit $result