tophat (2.1.1+dfsg1-1) unstable; urgency=medium * Team upload * debian/upstream/metadata: - Added references to registries - yamllint cleanliness [ Nadiya Sitdykova ] * add info about debian/tests/test_data [ Fabian Klötzl ] * remove convenience copy of samtools. Closes: #780816 * adapt tophat script to recent samtools version [ Andreas Tille ] * Remove unused license paragraph * Standards-Version: 4.1.1 * Really remove samtools code copy also from source tarball * Versioned Depends: samtools (>= 1.5) * d/watch: enable numbered dfsg-appendices -- Fabian Klötzl Wed, 06 Dec 2017 16:13:31 +0100 tophat (2.1.1+dfsg-4) unstable; urgency=medium * Build-Depends: bowtie + Architecture: any Closes: #873866 * Standards-Version: 4.1.0 (no changes needed) * Autoreconf is default with debhelper 10 -- Andreas Tille Mon, 04 Sep 2017 13:36:19 +0200 tophat (2.1.1+dfsg-3) unstable; urgency=medium * Team upload. [ Nadiya Sitdykova ] * Add autopkgtest test-suite [ Andreas Tille ] * debhelper 10 (use --no-parallel to avoid build problems) * Standards-Version: 4.0.0 (no changes needed) * Drop unneeded gbp.conf * d/rules: use DEB_SOURCE -- Nadiya Sitdykova Fri, 14 Jul 2017 21:15:50 -0400 tophat (2.1.1+dfsg-2) unstable; urgency=medium [ Sascha Steinbiss ] * Team upload. * Fix building with GCC 6. Closes: #811881. [ Andreas Tille ] * cme fix dpkg-control -- Sascha Steinbiss Sat, 14 May 2016 15:53:10 +0000 tophat (2.1.1+dfsg-1) unstable; urgency=medium * Imported Upstream version 2.1.1+dfsg * Refresh and delete unused patches * Apply cme fix dpkg * Export additional hardening flags - hardening=+all * Don't install 3rd party software (intervaltree,sortedcontainers) * Fix Makefile for the embedded copy of samtools-0.1.18 * d/copyright: - Add Files: stanza for samtools-0.1.18 - Add to Files-Excluded: intervaltree and sortedcontainers - Fix Source url -- Alexandre Mestiashvili Thu, 17 Mar 2016 14:22:58 +0100 tophat (2.1.0+dfsg-1) unstable; urgency=medium * New upstream version -- Andreas Tille Sat, 18 Jul 2015 17:42:53 +0200 tophat (2.0.14+dfsg-1) unstable; urgency=medium * Imported Upstream version 2.0.14+dfsg * d/patches: applied cme fix dpkg, s/Descriptions/Description/ -- Alexandre Mestiashvili Wed, 29 Apr 2015 15:10:10 +0200 tophat (2.0.13+dfsg-1) unstable; urgency=medium [ Andreas Tille ] * New upstream version * Adapted patches [ Alexandre Mestiashvili] * debian/patches/hardening4samtols.patch: add hardening flags for embedded copy of samtools -- Alexandre Mestiashvili Sun, 26 Oct 2014 15:53:02 +0100 tophat (2.0.12+dfsg-3) unstable; urgency=medium * Since tophat depends from bowtie|bowtie2 and now both versions are available only on amd64 tophat itself is also Architecture: amd64 kfreebsd-amd64 * Do not "Suggests: bowtie" since it is just in "Depends" * cme fix dpkg-control * d/copyright: fix "empty-short-license-in-dep5-copyright" lintian warnings -- Andreas Tille Thu, 25 Sep 2014 08:08:34 +0200 tophat (2.0.12+dfsg-2) unstable; urgency=medium * d/rules: - Fix syntax of uscan call - Remove redundant enforcement of xz compression * d/control: Versioned Build-Depends: seqan-dev (>= 1.4) Closes: #754664 -- Andreas Tille Fri, 22 Aug 2014 10:04:23 +0200 tophat (2.0.12+dfsg-1) unstable; urgency=medium [ Alexandre Mestiashvili ] * d/watch: new url * Imported Upstream version 2.0.12+dfsg * d/patches/fix_build_w_seqan1.4.patch: patch from Manuel Holtgrewe resolving #733352. removed const_ness_part1.patch as the new patch solves the problem completely Closes: #733352 * debian/patches/fix_includes_path.patch: exclude SeqAn-1.3 from configure.ac -- Alexandre Mestiashvili Thu, 03 Jul 2014 21:06:10 +0200 tophat (2.0.11+dfsg-1) UNRELEASED; urgency=medium * New upstream version * debian/copyright: Update contact * Move debian/upstream to debian/upstream/metadata * cme fix dpkg-control * debian/rules: - Make sure boost libraries will be found - some more invocations to help2man -- Andreas Tille Tue, 18 Mar 2014 13:54:41 +0100 tophat (2.0.10-1) unstable; urgency=low * Imported Upstream version 2.0.10 -- Alexandre Mestiashvili Thu, 21 Nov 2013 09:57:21 +0100 tophat (2.0.9-1) unstable; urgency=low * d/get-orig-source: place tarballs to ../tarballs/ * d/control: use canonical vcs fields, Standards-Version: 3.9.4 * d/changelog: updated source field * refreshed patches * Imported Upstream version 2.0.9 -- Alexandre Mestiashvili Thu, 04 Jul 2013 13:59:07 +0200 tophat (2.0.8b-1) unstable; urgency=low * Imported Upstream version 2.0.8b Closes: #707059 -- Alexandre Mestiashvili Tue, 07 May 2013 22:58:36 +0200 tophat (2.0.8-1) unstable; urgency=low * Imported Upstream version 2.0.8 -- Alexandre Mestiashvili Sat, 02 Mar 2013 12:38:32 +0100 tophat (2.0.7-1) unstable; urgency=low * Imported Upstream version 2.0.7 -- Alexandre Mestiashvili Sat, 23 Feb 2013 11:45:36 +0100 tophat (2.0.6-1) unstable; urgency=low * Team upload [ Carlos Borroto ] * Imported Upstream version 2.0.6 -- Charles Plessy Tue, 06 Nov 2012 14:54:31 +0900 tophat (2.0.5-1) unstable; urgency=low [ Alexandre Mestiashvili ] * Imported Upstream version 2.0.5 -- Alexandre Mestiashvili Fri, 05 Oct 2012 10:56:26 +0200 tophat (2.0.3-1) unstable; urgency=low * Imported Upstream version 2.0.3 -- Alexandre Mestiashvili Sat, 09 Jun 2012 11:06:21 +0200 tophat (2.0.0-2) unstable; urgency=low * debian/upstream: BibTeX conform author syntax * debian/patces/bashism_in_shell_script.patch: Fix bashism in shell script Closes: #671813 * debhelper 9 (control+compat) * debian/rules: Create some manpages using help2man -- Andreas Tille Sun, 06 May 2012 13:26:38 +0200 tophat (2.0.0-1) unstable; urgency=low [ Charles Plessy ] * YAML syntax correction [ Alexandre Mestiashvili ] * Imported Upstream version 2.0.0 * updated debian/patches * debian/control added libboost-thread-dev dependency, added bowtie2 to Suggests: * debian/control Standards-Version: 3.9.3 Depends: bowtie2 * debian/copyright updated Format, removed seqan copyright statements * debian/patches removed unneeded patches * debian/get-orig-source - removes shipped with tophat SeqAn files. -- Alexandre Mestiashvili Sat, 14 Apr 2012 12:47:32 +0200 tophat (1.4.1-2) unstable; urgency=low [ Carlos Borroto ] * added bowtie as a binary dependency * suggests cufflinks [ Andreas Tille ] * debian/control: Added myself to uploaders * debian/patches/remove_cflag_handling_in_configure.patch: Enable better support for different architectures (Thanks to Peter Michael Green for the patch) Closes: #660309 * debian/upstream: Added references -- Andreas Tille Sat, 18 Feb 2012 08:22:50 +0100 tophat (1.4.1-1) unstable; urgency=low * Team upload. * Initial upload to Debian archive. [ Carlos Borroto ] * New upstream release [ Charles Plessy ] * Corrected VCS URL. * Minor description changes. * Recommend bowtie. * debian/copyright: - Normalised with config-edit --application dpkg-copyright. - Documented SeqAn and m4 macros. * Merged patches bam2samtools and fix_includes_path.patch (same purpose). * Build-depend only on python. * Tighten build-dependancy on sequan-dev. -- Charles Plessy Mon, 06 Feb 2012 16:12:29 +0900 tophat (1.4.0-1) UNRELEASED; urgency=low * New upstream release - debian/patches/fix_undefined_reference.patch -- Carlos Borroto Tue, 10 Jan 2012 11:49:39 -0500 tophat (1.3.3-1) UNRELEASED; urgency=low TODO: * src/SeqAn-1.2 should be excluded - tophat depends on seqan library which already exists in debian [Alexandre Mestiashvili] * New upstream release * Removed dh-make template from watch file * Added initial copyright data , removed templates , added Source * debian/compat version 8 * debian/control - Maintainer: Debian Med Packaging Team - DM-Upload-Allowed: yes - Added myself to Uploaders: - added correct Vcs-Git , Vcs-Browser fields - Standards-Version: 3.9.2 - added build-dependency quilt - added seqan-dev as dependency * debian/rules - removed dh-make template * debian/control Added python dependency to binary package * debian/control Description shouldn't start with package name * debian/rules removed quilt patch management * Added DEP3 headers to patches. * Added Pre-Depends: dpkg (>= 1.15.6) (xz compression) Fixed syntax-error in debian/copyright -- Alexandre Mestiashvili Thu, 05 Jan 2012 14:37:19 +0100 tophat (1.3.1-1ppa1~lucid1) lucid; urgency=low * New upstream version -- Carlos Borroto Thu, 23 Jun 2011 11:02:22 -0400 tophat (1.3.0-1ppa1~lucid1) lucid; urgency=low * Backported to lucid -- Carlos Borroto Wed, 08 Jun 2011 14:56:32 -0400 tophat (1.3.0-1) UNRELEASED; urgency=low * Initial release * debian/patches/fix_includes_path.patch * debian/patches/fix-configure.patch -- Carlos Borroto Wed, 08 Jun 2011 14:34:56 -0400