[med-svn] [Git][med-team/picard-tools][master] 2 commits: fix manifest for runtime deps closes #919559

[Olivier Sallou]

Olivier Sallou pushed to branch master at Debian Med / picard-tools


Commits:
0724ae27 by Olivier Sallou at 2019-01-17T17:48:30Z
fix manifest for runtime deps closes #919559

- - - - -
c93e1866 by Olivier Sallou at 2019-01-17T17:48:30Z
set current investigation status

- - - - -


3 changed files:

- debian/bin/PicardCommandLine
- debian/changelog
- + debian/libpicard-java.manifest


Changes:

=====================================
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
=====================================
@@ -1,3 +1,11 @@
+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 at 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
=====================================
@@ -0,0 +1,3 @@
+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



View it on GitLab: https://salsa.debian.org/med-team/picard-tools/compare/077712af88da3e0f85fb1c3949b7c468b895577a...c93e1866f9549e899c8ce00549e94bd3b53f1804

-- 
View it on GitLab: https://salsa.debian.org/med-team/picard-tools/compare/077712af88da3e0f85fb1c3949b7c468b895577a...c93e1866f9549e899c8ce00549e94bd3b53f1804
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