picard-tools (3.3.0+dfsg-1) unstable; urgency=medium * New upstream version 3.3.0+dfsg * Refreshing patches * Raising Standards version to 4.7.0, no change * Refreshing dates in d/copyright * Updating the list of build-dependencies * Patching out code related to Google cloud services * Fixing test accuracy issue -- Pierre Gruet Thu, 26 Dec 2024 22:14:02 +0100 picard-tools (3.1.1+dfsg-1) unstable; urgency=medium * New upstream version 3.1.1+dfsg * Refreshing patches * Enabling the test with BarclayParser again * Patching out more code portions using google-nio -- Pierre Gruet Sat, 16 Dec 2023 22:38:31 +0100 picard-tools (3.0.0+dfsg-1) unstable; urgency=medium * New upstream version 3.0.0+dfsg * Refreshing patches * Raising Standards version to 4.6.2 (no change) * Removing unnecessary versioned B-D * Adding nashorn to d/maven.ignoreRules * Running the build-time tests from a directory with no '+' in its path * Omitting the long-failing jar invocation in the tests -- Pierre Gruet Tue, 04 Jul 2023 15:23:35 +0200 picard-tools (2.27.5+dfsg-2) unstable; urgency=medium * Stopping exporting ANT_HOME and JAVA_HOME in d/rules, this caused FTBFS on buildds since OpenJDK17 became the default JDK -- Pierre Gruet Sun, 06 Nov 2022 17:21:06 +0100 picard-tools (2.27.5+dfsg-1) unstable; urgency=medium * New upstream version 2.27.5+dfsg * Refreshing patches * Adding a versioned B-D on libhtsjdk-java because of a change in its ABI * Building against openjdk-17 (Closes: #1011156): - Skipping tests which cannot run because of old Gradle not providing --add-opens - Stopping shipping BamToBfq because of a byte change in BamToBfqTest when switching to OpenJDK17 * Marking the 60- patch as Forwarded: not-needed -- Pierre Gruet Fri, 04 Nov 2022 11:09:56 +0100 picard-tools (2.27.4+dfsg-1) unstable; urgency=medium * New upstream version 2.27.4+dfsg * Refreshing patches * Updating d/watch after a change in the Github layout * Refreshing the Lintian override for embedded Javascript -- Pierre Gruet Thu, 22 Sep 2022 20:25:58 +0200 picard-tools (2.27.2+dfsg-2) unstable; urgency=medium * Using maven_repo_helper to provide Maven artifacts -- Pierre Gruet Thu, 07 Jul 2022 16:28:40 +0200 picard-tools (2.27.2+dfsg-1) unstable; urgency=medium * New upstream version 2.27.2+dfsg * Refreshing patches * Raising Standards version to 4.6.1 (no change) * Switching from XmX4G to XmX2G in d/rules to enhance build on i386 * Omitting the build of classes concerned by the removal of the com.sun.javadoc package in OpenJDK 17 (Closes: #1013577) -- Pierre Gruet Sun, 26 Jun 2022 21:40:39 +0200 picard-tools (2.27.1+dfsg-1) unstable; urgency=medium * New upstream version 2.27.1+dfsg * Refreshing patches * Refreshing d/copyright -- Pierre Gruet Sun, 24 Apr 2022 07:11:18 +0200 picard-tools (2.26.10+dfsg-1) unstable; urgency=medium * New upstream version 2.26.10+dfsg * Refreshing patches -- Pierre Gruet Fri, 18 Feb 2022 14:27:22 +0100 picard-tools (2.26.6+dfsg-2) unstable; urgency=medium * Removing now useless versioned dependencies * Deleting the main class name in the jar invocation by PicardCommandLine -- Pierre Gruet Sat, 04 Dec 2021 10:21:59 +0100 picard-tools (2.26.6+dfsg-1) unstable; urgency=medium [ Pierre Gruet ] * New upstream version 2.26.6+dfsg * Information in d/README.source is outdated, removing the file * Raising Standards version to 4.6.0 (no change) * Refreshing d/copyright * Refreshing patches * Setting properly the classpath in the .manifest file, no jar list in PicardCommandLine (Closes: #989961) * Updating the list of dependencies * Correcting a type error in a test concerning Illumina data provider * Adding a Lintian override for the embedded javascript * Adding a dependency of the doc package in libjs-jquery (Closes: #989328) * Adding myself as uploader [ Andreas Tille ] * Fix typo in d/u/metadata -- Pierre Gruet Thu, 02 Dec 2021 21:00:23 +0100 picard-tools (2.24.1+dfsg-1) unstable; urgency=medium [ Andreas Tille ] * New upstream version * Do not delete "*.bai" files after testing [ Pierre Gruet ] * Correcting the data provider for test testActionsWithDontMergeAbutting -- Andreas Tille Thu, 28 Jan 2021 07:47:42 +0100 picard-tools (2.24.0+dfsg-1) unstable; urgency=medium * Team upload. * New upstream version * Standards-Version: 4.5.1 (routine-update) * refresh patches. TODO: test failures -- Michael R. Crusoe Thu, 07 Jan 2021 13:43:53 +0100 picard-tools (2.23.8+dfsg-3) unstable; urgency=medium * Team upload. * Oops, should have been Architecture: all everywhere -- Michael R. Crusoe Wed, 18 Nov 2020 12:19:16 +0100 picard-tools (2.23.8+dfsg-2) unstable; urgency=medium * Team upload. [ Steffen Moeller ] * New upstream version * Added link from /usr/lib/debian-med/bin/picard to PicardCommandLine only temporarily for now for presumed compatibility with what conda is offering and what bcbio is apparently expecting. * Added reference to d/u/metadata as suggested by upstream. [ Michael R. Crusoe ] * debian/patches/non-intel-skip-intel-tests: Skip two "Intel" specific tests on non-amd64 systems. * Switch to Architecture: all to match libgkl-java -- Michael R. Crusoe Wed, 18 Nov 2020 10:34:59 +0100 picard-tools (2.23.7+dfsg-1) unstable; urgency=medium * Team upload. * Mark libpicard-java-doc as Multi-Arch: foreign. Thanks multiarch hinter! * blhc: ignore false positives with gradle + *ScriptTransformer -- Michael R. Crusoe Wed, 14 Oct 2020 11:59:07 +0200 picard-tools (2.23.4+dfsg-3) unstable; urgency=medium * Team upload. * debian/tests/control: adjustments to avoid testing on non-amd64 Closes: #970502 * Mark the remaining patches as not needing forwarding to upstream. -- Michael R. Crusoe Thu, 08 Oct 2020 18:41:58 +0200 picard-tools (2.23.4+dfsg-2) unstable; urgency=medium * Fixed classpath in picard.jar Manifest (s/:/ /g) -- Steffen Moeller Fri, 11 Sep 2020 23:40:02 +0200 picard-tools (2.23.4+dfsg-1) unstable; urgency=medium [ Michael R. Crusoe ] * Standards-Version: 4.5.0 (routine-update) * debhelper-compat 13 (routine-update) * Refresh patches * Remove trailing whitespace in debian/changelog (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Trim trailing whitespace. * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. [ Andreas Tille ] * New upstream version * Remove redundant debian/gbp.conf -- Andreas Tille Thu, 10 Sep 2020 17:43:02 +0200 picard-tools (2.22.8+dfsg-1) unstable; urgency=medium * New upstream release * Source only upload Closes: #961865 -- Olivier Sallou Fri, 29 May 2020 08:25:43 +0000 picard-tools (2.18.25+dfsg-3) unstable; urgency=medium * Remove libguava-java-doc dependency (Closes: #961700). * debian/patches/60-tests-exclude-network.patch remove test needing network hostname resolution -- Olivier Sallou Fri, 29 May 2020 07:11:48 +0000 picard-tools (2.18.25+dfsg-2) unstable; urgency=medium * Architecture amd64 (for libpicard-java and picard-tools) Closes: #921185 * Remove trailing whitespace in debian/changelog -- Andreas Tille Sun, 03 Feb 2019 08:53:09 +0100 picard-tools (2.18.25+dfsg-1) unstable; urgency=medium * New upstream release -- Olivier Sallou Fri, 25 Jan 2019 10:46:36 +0000 picard-tools (2.18.23+dfsg-2) unstable; urgency=medium * Fix Class-Path in manifest file for dependencies (Closes: #919559). -- Olivier Sallou Thu, 17 Jan 2019 15:54:27 +0000 picard-tools (2.18.23+dfsg-1) unstable; urgency=medium * New upstream version * debhelper 12 * Standards-Version: 4.3.0 -- Andreas Tille Fri, 11 Jan 2019 22:52:33 +0100 picard-tools (2.18.17+dfsg-1) unstable; urgency=medium [ Emmanuel Bourg ] * Fixed the build failure with Java 11 Closes: #915898, #880258 [ Andreas Tille ] * New upstream version * Secure URI in copyright format * Remove trailing whitespace in debian/changelog * Remove trailing whitespace in debian/control * Remove trailing whitespace in debian/rules * Add ALIGNMENT_STATUS=All to command line Closes: #905645 -- Andreas Tille Wed, 12 Dec 2018 09:06:37 +0100 picard-tools (2.18.14+dfsg-1) unstable; urgency=medium * New upstream version * Standards-Version: 4.2.1 * Fix link Closes: #905706 * Versioned Build-Depends: libhtsjdk-java (>= 2.16.1~) * d/rules: Respect DEB_BUILD_OPTIONS in override_dh_auto_test * Simplified d/copyright by not mentioning every single file -- Andreas Tille Wed, 19 Sep 2018 09:20:48 +0200 picard-tools (2.18.2+dfsg-1) unstable; urgency=medium * New upstream version * Backports-friendly debhelper 11 * Bump versioned Build-Depends on libhtsjdk-java and default-jdk [O. Sallou] * Java 9/10 fixes * Remove Google NIO support (not packaged in Debian) * Enable unit tests after jcommander fix -- Andreas Tille Tue, 17 Apr 2018 22:45:38 +0200 picard-tools (2.8.1+dfsg-4) unstable; urgency=medium * Team upload. * Fixed the build failure with Java 9 (Closes: #894329) * Standards-Version updated to 4.1.4 * Switch to debhelper level 11 * Use salsa.debian.org Vcs-* URLs -- Emmanuel Bourg Fri, 06 Apr 2018 17:36:09 +0200 picard-tools (2.8.1+dfsg-3) unstable; urgency=medium * debian/upstream/metadata: RRID -> SciCrunch [ Olivier Sallou ] * d/patches/40-tests-fix-testng.patch: fix testng reference * d/rules: disable unit tests due to gradle 3.2+testng issue (will be fixed by gradle 3.4), lower #880258 severity -- Steffen Moeller Sun, 22 Oct 2017 18:38:46 +0200 picard-tools (2.8.1+dfsg-2) unstable; urgency=medium * Team upload. * Add simple autopkgtest test-suite Closes: #848334 * Add README.test -- Nadiya Sitdykova Fri, 31 Mar 2017 01:15:20 -0400 picard-tools (2.8.1+dfsg-1) unstable; urgency=medium [ Vincent Danjean ] * Ensure versioned B-D and Depends are in sync [ Andreas Tille ] * New upstream version -- Andreas Tille Tue, 10 Jan 2017 11:20:45 +0100 picard-tools (2.8.0+dfsg-2) unstable; urgency=medium * Fix versioned Depends Closes: #848831 -- Andreas Tille Tue, 20 Dec 2016 08:52:21 +0100 picard-tools (2.8.0+dfsg-1) unstable; urgency=medium [ Andreas Tille ] * New upstream version * debhelper 10 * d/watch: version=4 * Ensure that major version of htsjdk is 2.8 [ Vincent Danjean ] * Really force C locale for tests * Fix parameter type for one test * cleanup generated test files -- Andreas Tille Sun, 18 Dec 2016 19:29:34 +0100 picard-tools (2.7.1+dfsg-2) unstable; urgency=medium * Rebuild with htsjdk 2.7 * Ensure for build and runtime that major versions of picard-tools and htsjdk are the same. -- Vincent Danjean Sun, 27 Nov 2016 21:01:25 +0100 picard-tools (2.7.1+dfsg-1) unstable; urgency=medium * New upstream version -- Andreas Tille Thu, 27 Oct 2016 17:10:08 +0200 picard-tools (2.6.0+dfsg-1) unstable; urgency=medium * Team upload. [ Andreas Tille ] * New upstream version * Bump versioned dependency of libhtsjdk-java * d/copyright: remove *.bak files which are removed in clean target anyway [ Vincent Danjean ] * Avoid warnings when running PicardCommandLine [ Sascha Steinbiss ] * Patch build.gradle to remove shadowJar. * Fix test case with mismatching data provider and test method. * Drop unneeded jh_installlibs override. * Remove duplicated build-deps. -- Sascha Steinbiss Sat, 10 Sep 2016 15:55:28 +0000 picard-tools (2.5.0-gradle+dfsg-1) unstable; urgency=medium * New upstream release * Switch to gradle build system -- Vincent Danjean Thu, 07 Jul 2016 10:21:33 +0200 picard-tools (2.1.1+dfsg-1) unstable; urgency=medium * New upstream version * Adapt debian/watch to use xz compression * Remove Shaun Jackman and add myself as Uploader * cme fix dpkg-control [ Steffen Moeller and Jon Ison ] * Added EDAM annotation to debian/upstream/edam -- Andreas Tille Tue, 05 Apr 2016 09:59:27 +0200 picard-tools (1.138+dfsg.1-1) unstable; urgency=medium * New release from new upstream location (github). Closes: #798051 * Full reorganization of the packaging -- Vincent Danjean Tue, 08 Sep 2015 11:15:42 +0200 picard-tools (1.113-2) unstable; urgency=medium * Team upload. * Replaced the dependency on libsnappy1.0.3-java with libsnappy-java. * Standards-Version updated to 3.9.6 (no changes) -- Emmanuel Bourg Wed, 02 Sep 2015 13:10:32 +0200 picard-tools (1.113-1) unstable; urgency=medium * New upstream release 1.113 -- Olivier Sallou Fri, 06 Jun 2014 23:27:25 +0200 picard-tools (1.110-1) unstable; urgency=medium * Imported Upstream version 1.110. * Normalised debian/control with config-model-edit. * Refreshed patch ‘use_libjbzip2-java’. -- Charles Plessy Sun, 06 Apr 2014 10:56:12 +0900 picard-tools (1.109-1) unstable; urgency=medium * Imported Upstream versions 1.106, 1.107, 1.108 and 1.109. -- Charles Plessy Sat, 22 Mar 2014 11:35:22 +0900 picard-tools (1.105-1) unstable; urgency=low * New upstream release 1.105 * Conforms with Policy 3.9.5. -- Olivier Sallou Tue, 24 Dec 2013 11:16:18 +0100 picard-tools (1.100-1) unstable; urgency=low [Charles Plessy] * Imported Upstream version 1.100 * Compress the source archive with XZ. * Mark the use of git-buildpackage and pristine-tar with a gbp.conf file. [Olivier Sallou] * d/rules: fix build for release -- Charles Plessy Sun, 20 Oct 2013 10:38:11 +0900 picard-tools (1.95-1) unstable; urgency=low * New upstream release * Fix man page with missing tools from previous releases * Fix picard-tools binary to manage missing tools from previous releases * Fix management of JAVA_OPTIONS if not set at all. -- Olivier Sallou Thu, 25 Jul 2013 13:36:02 +0200 picard-tools (1.90-3) unstable; urgency=low * Add possibility to specify JAVA options (Closes: #705681), with JAVA_OPTIONS env variable. -- Olivier Sallou Tue, 09 Jul 2013 09:20:07 +0200 picard-tools (1.90-2) unstable; urgency=low * Load in unstable, all deps are available. -- Olivier Sallou Sun, 02 Jun 2013 10:57:05 +0200 picard-tools (1.90-1) experimental; urgency=low * New upstream release -- Olivier Sallou Wed, 01 May 2013 13:57:05 +0200 picard-tools (1.87-1) experimental; urgency=low * New upstream release -- Olivier Sallou Wed, 01 May 2013 15:14:04 +0100 picard-tools (1.82-2) unstable; urgency=low * Fix classpath for BuildBamIndex (Closes: #705686). -- Olivier Sallou Fri, 19 Apr 2013 14:26:23 +0200 picard-tools (1.82-1) unstable; urgency=low * New upstream release -- Olivier Sallou Thu, 03 Jan 2013 10:46:26 +0100 picard-tools (1.80-1) unstable; urgency=low * New upstream release -- Olivier Sallou Sun, 02 Dec 2012 23:10:10 +0100 picard-tools (1.79-1) unstable; urgency=low * New upstream release 1.79 -- Olivier Sallou Mon, 29 Oct 2012 08:58:44 +0100 picard-tools (1.78-1) unstable; urgency=low * New upstream release -- Olivier Sallou Sat, 13 Oct 2012 11:20:49 +0200 picard-tools (1.77-1) unstable; urgency=low * New upstream release -- Olivier Sallou Fri, 21 Sep 2012 16:41:23 +0200 picard-tools (1.76-1) unstable; urgency=low * New upstream release -- Olivier Sallou Fri, 07 Sep 2012 11:44:03 +0200 picard-tools (1.75-1) unstable; urgency=low [Olivier Sallou] * New upstream releases. * Build-depend on libsnappy1.0.3-java (debian/control). [Charles Plessy] * Refreshed debian/patches/01-build.xml. * Use default java implementation. - debian/control: BD on default-jdk, switch runtime dependency to default-jre | java6-runtime. - debian/rules: Specify source/target = 1.5 to ensure that backwards compatible bytecode is built. - Closes: #684172, thanks to J. Page and Ubuntu. -- Olivier Sallou Thu, 06 Sep 2012 09:10:11 +0900 picard-tools (1.46-1) unstable; urgency=low * New upstream release. * Depend on ${python:Depends} (debian/changelog). * Incremented Standards-Version to reflect conformance with Policy 3.9.2 (debian/changelog, no changes needed). * Corrected and validated debian/copyright machine-readable format. -- Charles Plessy Fri, 03 Jun 2011 20:50:00 +0900 picard-tools (1.41-1) unstable; urgency=low * New upstream release. Closes: #619201. * Add five commands to bin/picard-tools and picard-tools.1. -- Shaun Jackman Tue, 22 Mar 2011 10:52:23 -0700 picard-tools (1.27-1) unstable; urgency=low * New upstream release. * Incremented Standards-Version to reflect conformance with Policy 3.9.1 (debian/changelog, no changes needed). -- Charles Plessy Tue, 03 Aug 2010 20:20:10 +0900 picard-tools (1.25-1) unstable; urgency=low * New upstream release. -- Shaun Jackman Tue, 06 Jul 2010 16:06:18 -0700 picard-tools (1.24-1) UNRELEASED; urgency=low * Initial release. Closes: #586015. -- Shaun Jackman Tue, 15 Jun 2010 10:41:09 -0700