debian/bin/PicardCommandLine

@@ -12,4 +12,6 @@ PicardCommandLine)
 	;;
 esac
 export USE_LIBRARY_PATH=USE_LIBRARY_PATH
-exec java ${JAVA_OPTIONS-} -jar /usr/share/java/picard.jar "$@"
+export PICARD_CLASSPATH=/usr/share/java/picard.jar:/usr/share/java/htsjdk.jar:/usr/share/java/guava.jar:/usr/lib/jvm/default-java/lib/tools.jar:/usr/share/java/commons-lang3.jar:/usr/share/java/gkl.jar:/usr/share/java/gatk-native-bindings.jar:/usr/share/java/barclay.jar
+
+exec java ${JAVA_OPTIONS-} -cp $PICARD_CLASSPATH picard.cmdline.PicardCommandLine "$@"

debian/changelog

+picard-tools (2.18.23+dfsg-2) UNRELEASE; urgency=medium
+
+  * Fix Class-Path in manifest file for dependencies  (Closes: #919559).
+   [TODO] 2 tests are still failing with autopkgtest though source build
+   and testing works fine.
+
+ -- Olivier Sallou <osallou@debian.org>  Thu, 17 Jan 2019 15:54:27 +0000
+
 picard-tools (2.18.23+dfsg-1) unstable; urgency=medium
 
   * New upstream version

debian/libpicard-java.manifest

+usr/share/java/picard.jar:
+  Main-Class: picard.cmdline.PicardCommandLine
+  Class-Path: /usr/share/java/htsjdk.jar:/usr/share/java/guava.jar:/usr/lib/jvm/default-java/lib/tools.jar:/usr/share/java/commons-lang3.jar:/usr/share/java/gkl.jar:/usr/share/java/gatk-native-bindings.jar:/usr/share/java/barclay.jar