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debian/artemis.install
View file @ c79e7be1
jar_build/artemis.jar usr/share/java/
jar_build/act.jar usr/share/java/
jar_build/bamview.jar usr/share/java/
jar_build/DNAPlotter.jar usr/share/java/
jar_build/dnaplotter.jar usr/share/java/
debian/desktop/*.desktop usr/share/applications/
images/helix.png usr/share/icons/hicolor/96x96/apps/
debian/artemis.links
View file @ c79e7be1
usr/share/java/artemis.jar usr/bin/art
usr/share/java/act.jar usr/bin/act
usr/share/java/DNAPlotter.jar usr/bin/dnaplotter
usr/share/java/dnaplotter.jar usr/bin/dnaplotter
usr/share/java/bamview.jar usr/bin/bamview
debian/artemis.manifest.in
View file @ c79e7be1
......@@ -10,7 +10,7 @@
Class-Path: @CLASSPATH@
Main-Class: uk.ac.sanger.artemis.components.alignment.BamView
Permissions: all-permissions
/usr/share/java/DNAPlotter.jar:
/usr/share/java/dnaplotter.jar:
Class-Path: @CLASSPATH@
Main-Class: uk.ac.sanger.artemis.circular.DNADraw
Permissions: all-permissions
debian/changelog
View file @ c79e7be1
artemis (17.0.1+dfsg-1) UNRELEASED; urgency=medium
artemis (17.0.1+dfsg-1) unstable; urgency=medium
* Team upload.
* New upstream version
......@@ -9,8 +9,10 @@ artemis (17.0.1+dfsg-1) UNRELEASED; urgency=medium
* Class FTPSeekableStream should not be excluded
* Update patch that prevents copying of non-existing files
* d/rules: Use dh_auto_build instead of $(MAKE)
* All JAR files named lower case according to Java policy
* d/watch: use xz compression
-- Andreas Tille <tille@debian.org> Sat, 17 Mar 2018 11:41:38 +0100
-- Andreas Tille <tille@debian.org> Tue, 14 Aug 2018 13:59:24 +0200
artemis (16.0.17+dfsg-3) unstable; urgency=medium
......
debian/control
View file @ c79e7be1
......@@ -22,6 +22,7 @@ Build-Depends: debhelper (>= 11~),
ant-optional,
junit4,
libhamcrest-java,
libjs-jquery,
# To convert gifs to png because gif is not a supported icon format
imagemagick
Standards-Version: 4.2.0
......
debian/copyright
View file @ c79e7be1
......@@ -5,6 +5,7 @@ Source: https://github.com/sanger-pathogens/Artemis
Files-Excluded:
lib/*
test/lib/*
*/jquery.js
Files: *
Copyright: 1998-2013 Genome Research Limited
......
debian/patches/jar-rules.patch
View file @ c79e7be1
......@@ -48,8 +48,9 @@ Last-Update: Sun, 05 Aug 2018 07:16:40 +0200
+ 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 \
- 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; \
+ jar cmf manifest-circular ../dnaplotter.jar images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg README.md etc \
+ org uk ; \
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; \
......
debian/rules
View file @ c79e7be1
......@@ -44,7 +44,14 @@ override_dh_auto_build:
convert images/helix.gif -resize 96x96\! images/helix.png
override_dh_auto_test:
cd test && ant -f build-test.xml run-manual-tests-headless -DEMBOSS_ROOT=/usr
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
ln -s /usr/share/javascript/jquery/jquery.js test/coverage-report/evosuite-auto-tests/files/jquery.js
ln -s /usr/share/javascript/jquery/jquery.js test/coverage-report/evosuite-auto-tests/html/files/jquery.js
mkdir lib
cd test && ant -f build-test.xml run-manual-tests-headless -DEMBOSS_ROOT=/usr # || true
rm -rf lib
rm test/coverage-report/evosuite-auto-tests/files/jquery.js test/coverage-report/evosuite-auto-tests/html/files/jquery.js
endif
override_dh_auto_clean:
dh_auto_clean
......
debian/watch
View file @ c79e7be1
version=4
opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg$//,filenamemangle=s/(?:.*)?v?(\d[\d\.]*)\.tar\.gz/artemis-$1.tar.gz/" \
opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg$//,filenamemangle=s/(?:.*)?v?(\d[\d\.]*)\.tar\.gz/artemis-$1.tar.gz/,repack,compression=xz" \
https://github.com/sanger-pathogens/Artemis/releases (?:.*/)?v?(\d[\d\.]*)\.tar\.gz