From c367f6a2fdf7941382bf9cb209834e96caec0c40 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E2=80=9Ckpepper=E2=80=9D?= <kp11@sanger.ac.uk>
Date: Mon, 15 Oct 2018 11:09:26 +0100
Subject: [PATCH] Changed to use absolute paths rather than relative
---
ChangeLog | 10 ++++++----
act | 2 +-
art | 2 +-
bamview | 2 +-
dnaplotter | 2 +-
etc/writedb_entry | 11 +++++------
src/assembly/unix-release-assembly.xml | 9 +++++++++
7 files changed, 24 insertions(+), 14 deletions(-)
diff --git a/ChangeLog b/ChangeLog
index 9c7cc1480..b5f125458 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,12 +1,14 @@
Version 18
1) Switched build process to use Maven. Changed directory structure. Removed ant and Make files.
- 2) Retired a number of jars and upgraded others. Removed the ssh plugin jar as it's not used.
+ 2) Retired a number of jars and upgraded others. Removed the ssh-plugin jar.
3) Upgraded to Picard 2.18.14 jar, which has a number of important bug fixes.
- 4) Removed old documentation functionality. HTML/PDF manuals are now stored in gh-pages and generated from a word doc.
- 5) Changed application scripts jar paths.
+ 4) Removed old documentation functionality. HTML/PDF manuals are now stored in gh-pages branch and exported directly from a word doc.
+ 5) Changed application script jar paths.
6) Rewrote writedb_entry script.
- 7)
+ 7) Replaced script usage of -Dcom.apple.mrj.application.apple.menu.about.name with -Xdock:name.
+ 8) Fixed incorrect Amigo GO term URL, used in the Artemis gene builder window.
+ 9) Updated README.
Version 17.0.2-test - patch release for Sanger. Changes incorporated into GitHub master.
diff --git a/act b/act
index 02cd51e22..882862501 100755
--- a/act
+++ b/act
@@ -138,7 +138,7 @@ then
echo "Starting ACT with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
fi
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp ".:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.ActMain $*
+$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.ActMain $*
result=$?
exit $result
diff --git a/art b/art
index f3413f1e6..85930e5a1 100755
--- a/art
+++ b/art
@@ -144,7 +144,7 @@ then
echo "Starting Artemis with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
fi
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp ".:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.ArtemisMain $*
+$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.ArtemisMain $*
result=$?
exit $result
diff --git a/bamview b/bamview
index 30b8d603d..cf64667a0 100755
--- a/bamview
+++ b/bamview
@@ -82,7 +82,7 @@ then
echo "Starting BamView with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
fi
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp ".:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.alignment.BamView $*
+$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.alignment.BamView $*
result=$?
exit $result
diff --git a/dnaplotter b/dnaplotter
index a0f36b4c0..fe9e835fa 100755
--- a/dnaplotter
+++ b/dnaplotter
@@ -119,7 +119,7 @@ then
echo "Starting DNA Plotter with arguments: $FLAGS $APPLICATION_PROPERTIES $TEMPLATE_FILE_ARG"
fi
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp ".:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.circular.DNADraw $TEMPLATE_FILE_ARG
+$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.circular.DNADraw $TEMPLATE_FILE_ARG
result=$?
exit $result
diff --git a/etc/writedb_entry b/etc/writedb_entry
index 1fccd24b1..60c9e46cc 100755
--- a/etc/writedb_entry
+++ b/etc/writedb_entry
@@ -6,9 +6,8 @@
# writedb_entry -help
# writedb_entry -s Pf3D7_01 Pf3D7_05 Pf3D7_07
#
-# The Java JRE to use is taken from the ARTEMIS_JAVA_JRE
-# environment variable. If this is not set then the JRE is defaulted to
-# a Java 8 version.
+# If the environment variable ARTEMIS_JAVA_JRE points to a Java JRE
+# then this JRE will be used in preference to any other.
#
QUIET=no
@@ -55,7 +54,8 @@ FLAGS="-mx2048m -ms20m -Djdbc.drivers=org.postgresql.Driver -Dibatis"
DEFAULT_CONNECTION="-Dchado=db.genedb.org:5432/snapshot?genedb_ro -Dread_only"
APPLICATION_HOME=`dirname "$PRG"`/..
JAR_NAME=artemis.jar
-JAR_FILE=$APPLICATION_HOME/target/unix-jars/$JAR_NAME
+JAR_FILE_DEFAULT=$APPLICATION_HOME/target/unix-jars/$JAR_NAME
+JAR_FILE_INSTALLED=$APPLICATION_HOME/$JAR_NAME
#
# Use a custom Java version if necessary
@@ -106,10 +106,9 @@ done
if [[ "$QUIET" = "no" ]]
then
echo "Starting writedb_entry with arguments: $PROXY_SETTINGS $DEFAULT_CONNECTION $FLAGS $@"
- echo "Classpath: $CLASSPATH"
fi
-$JAVA $PROXY_SETTINGS $DEFAULT_CONNECTION $FLAGS -cp "$JAR_FILE" uk.ac.sanger.artemis.io.ReadAndWriteEntry "$@"
+$JAVA $PROXY_SETTINGS $DEFAULT_CONNECTION $FLAGS -cp "$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.io.ReadAndWriteEntry "$@"
result=$?
exit $result
diff --git a/src/assembly/unix-release-assembly.xml b/src/assembly/unix-release-assembly.xml
index 543f5a682..e2a3d2b10 100644
--- a/src/assembly/unix-release-assembly.xml
+++ b/src/assembly/unix-release-assembly.xml
@@ -21,6 +21,15 @@
<include>*.jar</include>
</includes>
</fileSet>
+ <fileSet>
+ <outputDirectory>${unix.assembly.folder}</outputDirectory>
+ <includes>
+ <include>etc/**</include>
+ </includes>
+ <directoryMode>0755</directoryMode>
+ <fileMode>0755</fileMode>
+ <lineEnding>unix</lineEnding>
+ </fileSet>
<fileSet>
<outputDirectory>${unix.assembly.folder}</outputDirectory>
<includes>
--
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