debian/artemis.install

 jar_build/artemis.jar usr/share/java/
 jar_build/act.jar     usr/share/java/
-jar_build/BamView.jar usr/share/java/
+jar_build/bamview.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

 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/BamView.jar	usr/bin/bamview
+usr/share/java/bamview.jar	usr/bin/bamview

debian/artemis.manifest.in

@@ -6,7 +6,7 @@
  Class-Path: @CLASSPATH@
  Main-Class: uk.ac.sanger.artemis.components.ActMain
  Permissions: all-permissions
-/usr/share/java/BamView.jar:
+/usr/share/java/bamview.jar:
  Class-Path: @CLASSPATH@
  Main-Class: uk.ac.sanger.artemis.components.alignment.BamView
  Permissions: all-permissions

debian/patches/jar-rules.patch

@@ -50,7 +50,7 @@ Last-Update:   Sun, 05 Aug 2018 07:16:40 +0200
      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 joptsimple ngs freemarker ; \
++                         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; \
 +	jar cmf manifest-bamview ../bamview.jar etc org uk ; \

debian/patches/series

@@ -3,3 +3,4 @@ jar-rules.patch
 test-classpath.patch
 samreader.patch
 use-lang3.patch
+fix-test.patch

debian/rules

@@ -44,7 +44,7 @@ override_dh_auto_build:
 	convert images/helix.gif -resize 96x96\! images/helix.png
 
 override_dh_auto_test:
-	cd test && ant -f build-test.xml -DEMBOSS_ROOT=/usr
+	cd test && ant -f build-test.xml run-manual-tests-headless -DEMBOSS_ROOT=/usr
 
 override_dh_auto_clean:
 	dh_auto_clean