debian/changelog

-ipig (0.0.r5-3) UNRELEASED; urgency=medium
+ipig (0.0.r5-3) unstable; urgency=medium
 
+  [ Steffen Moeller ]
   * debian/upstream/metadata: Added refs to registries
 
- -- Steffen Moeller <moeller@debian.org>  Thu, 03 Aug 2017 13:37:12 +0200
+  [ Andreas Tille ]
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.1.4
+  * Java Policy conform versioning of JAR
+
+ -- Andreas Tille <tille@debian.org>  Wed, 04 Jul 2018 10:24:12 +0200
 
 ipig (0.0.r5-2) unstable; urgency=medium
 

debian/compat

-9
+11

debian/control

 Source: ipig
-Section: science
-Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille@debian.org>
-Build-Depends: debhelper (>= 9),
-               javahelper (>=0.25),
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 11~),
+               javahelper,
                default-jdk,
                ant,
                libcommons-compress-java,
                libcommons-net-java,
                libjdom1-java,
                libxerces2-java
-Standards-Version: 3.9.5
-Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/ipig.git
-Vcs-Git: git://anonscm.debian.org/debian-med/ipig.git
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/ipig
+Vcs-Git: https://salsa.debian.org/med-team/ipig.git
 Homepage: http://sourceforge.net/projects/ipig/
 
 Package: ipig
 Architecture: any
 Depends: ${misc:Depends},
-         ${java:Depends},
+         ${java:Depends}
 Description: integrating PSMs into genome browser visualisations
  iPiG targets the integration of peptide spectrum matches (PSMs) from
  mass spectrometry (MS) peptide identifications into genomic

debian/rules

@@ -2,7 +2,8 @@
 
 # DH_VERBOSE := 1
 
-SRC_VERSION =$(shell dpkg-parsechangelog | sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p')
+include /usr/share/dpkg/default.mk
+#jarversion=$(shell echo $(DEB_VERSION_UPSTREAM) | sed 's/r//')
 
 export JAVA_HOME=/usr/lib/jvm/default-java
 
@@ -22,6 +23,11 @@ override_dh_install:
 
 override_dh_auto_build:
 	cp debian/build.xml build.xml
-	sed -i "s/DEBVERSION/"$(SRC_VERSION)"/g" build.xml
+#	sed -i "s/DEBVERSION/$(jarversion)/g" build.xml
+	sed -i "s/DEBVERSION/$(DEB_VERSION_UPSTREAM)/g" build.xml
 	dh_auto_build
 
+#override_jh_installlibs:
+#	jh_installlibs
+#	mv debian/$(DEB_SOURCE)/usr/share/java/iPiG-$(DEB_VERSION_UPSTREAM).jar debian/$(DEB_SOURCE)/usr/share/java/iPiG-$(jarversion).jar
+#	ln -sf iPiG-$(jarversion).jar debian/$(DEB_SOURCE)/usr/share/java/iPiG.jar