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debian/changelog
View file @ 551ab850
......@@ -7,6 +7,8 @@ artemis (17.0.1+dfsg-1) UNRELEASED; urgency=medium
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.0
* Class FTPSeekableStream should not be excluded
* Update patch that prevents copying of non-existing files
* d/rules: Use dh_auto_build instead of $(MAKE)
-- Andreas Tille <tille@debian.org> Sat, 17 Mar 2018 11:41:38 +0100
......
debian/patches/jar-rules.patch
View file @ 551ab850
......@@ -4,48 +4,61 @@ Description: Leave out removed files when building jar files
Their absence causes "can not stat" errors, so any reference to
them is removed here.
Author: Afif Elghraoui <afif@ghraoui.name>
Andreas Tille <tille@debian.org>
Forwarded: not-needed
Last-Update: 2015-10-22
Last-Update: Sun, 05 Aug 2018 07:16:40 +0200
--- a/Makefile
+++ b/Makefile
@@ -75,6 +75,7 @@ artemis.jar : $(CLASSES)
@@ -75,27 +75,7 @@ artemis.jar : $(CLASSES)
mkdir -p jar_build/build
rm -f *.jar
cd jar_build/build; \
+ if [ "$$BUILDSYSEM" = "not-Debian" ] ; then \
for fileJar in ../../lib/*.jar; do \
jar xvf $$fileJar; \
rm -rf META-INF/MANIFEST.MF; \
@@ -96,7 +97,11 @@ artemis.jar : $(CLASSES)
rm -rf META-INF/MANIFEST.MF; \
done; \
cp -R ../../lib/LICENSE.* ../../uk ../../org ../../etc ../../images ../../lib/j2ssh/j2ssh.properties \
- ../../images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg ../../images/icon.gif ../../README.md ../../artemis_sqlmap .
+ ../../images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg ../../images/icon.gif ../../README.md ../../artemis_sqlmap . \
+ else \
+ cp -R ../uk ../org ../nsdb ../type ../seqdb ../etc ../images \
+ ../images/PSUlogo.gif ../images/icon.gif ../README.md ../artemis_sqlmap . ; \
+ fi
- for fileJar in ../../lib/*.jar; do \
- jar xvf $$fileJar; \
- rm -rf META-INF/MANIFEST.MF; \
- done; \
- for fileJar in ../../lib/j2ssh/*.jar; do \
- jar xvf $$fileJar; \
- rm -rf META-INF/MANIFEST.MF; \
- done; \
- for fileJar in ../../lib/ibatis/*.jar; do \
- jar xvf $$fileJar; \
- rm -rf META-INF/MANIFEST.MF; \
- done; \
- for fileJar in ../../lib/batik/*.jar; do \
- jar xvf $$fileJar; \
- rm -rf META-INF/MANIFEST.MF; \
- done; \
- for fileJar in ../../lib/picard/*.jar; do \
- jar xvf $$fileJar; \
- rm -rf META-INF/MANIFEST.MF; \
- done; \
- cp -R ../../lib/LICENSE.* ../../uk ../../org ../../etc ../../images ../../lib/j2ssh/j2ssh.properties \
+ cp -R ../../uk ../../org ../../etc ../../images \
../../images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg ../../images/icon.gif ../../README.md ../../artemis_sqlmap .
find jar_build/build -name '*.java' -print | xargs rm -f
find jar_build/build -name '.svn' -print | xargs rm -rf
find jar_build/build -name '*.DS_Store' -print | xargs rm -rf
@@ -104,15 +109,15 @@ artemis.jar : $(CLASSES)
@@ -103,16 +83,16 @@ artemis.jar : $(CLASSES)
cd jar_build/build; \
rm -rf META-INF/MANIFEST.MF; \
echo "Main-Class: uk.ac.sanger.artemis.components.ArtemisMain\nPermissions: all-permissions" > manifest-art; \
jar cmf manifest-art ../artemis.jar META-INF/services images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \
- jar cmf manifest-art ../artemis.jar META-INF/services images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \
- artemis_sqlmap org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE j2ssh.properties; \
+ artemis_sqlmap org uk com net htsjdk picard gov joptsimple ngs freemarker ; \
+ jar cmf manifest-art ../artemis.jar images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \
+ artemis_sqlmap org uk ; \
echo "Main-Class: uk.ac.sanger.artemis.circular.DNADraw\nPermissions: all-permissions" > manifest-circular; \
jar cmf manifest-circular ../DNAPlotter.jar images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg README.md etc \
- org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE j2ssh.properties; \
+ org uk com net htsjdk picard gov joptsimple ngs freemarker ; \
+ org uk joptsimple ngs freemarker ; \
echo "Main-Class: uk.ac.sanger.artemis.components.alignment.BamView\nPermissions: all-permissions" > manifest-bamview; \
- jar cmf manifest-bamview ../bamview.jar META-INF/services etc org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE; \
+ jar cmf manifest-bamview ../bamview.jar META-INF/services etc org uk com net htsjdk picard gov joptsimple ngs freemarker ; \
+ jar cmf manifest-bamview ../bamview.jar etc org uk ; \
echo "Main-Class: uk.ac.sanger.artemis.components.ActMain\nPermissions: all-permissions" > manifest-act; \
jar cmf manifest-act ../act.jar META-INF/services images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \
- jar cmf manifest-act ../act.jar META-INF/services images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \
- artemis_sqlmap org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE j2ssh.properties; \
+ artemis_sqlmap org uk com net htsjdk picard gov joptsimple ngs freemarker ; \
+ jar cmf manifest-act ../act.jar images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \
+ artemis_sqlmap org uk ; \
rm -rf jar_build/build;
debian/rules
View file @ 551ab850
......@@ -38,14 +38,13 @@ export CLASSPATH := $(subst $(space),:,$(strip $(CLASSPATH)))
dh $@ --with javahelper
override_dh_auto_build:
$(MAKE) jar
# dh_auto_build -- jar # does not work since the build does not find all plain files that should be include in jar since it cds to subdir first
dh_auto_build -- jar
sed 's|@CLASSPATH@|$(subst :,$(space),$(subst $(CURDIR),/usr/share/java/artemis.jar,$(CLASSPATH)))|g' debian/artemis.manifest.in > \
debian/artemis.manifest
convert images/helix.gif -resize 96x96\! images/helix.png
override_dh_auto_test:
cd test && ant -f build-test.xml test-headless -DEMBOSS_ROOT=/usr
cd test && ant -f build-test.xml -DEMBOSS_ROOT=/usr
override_dh_auto_clean:
dh_auto_clean
......