bowtie2 (2.5.0-3) unstable; urgency=medium
* Merge all autopkgtest scripts into run-unit-test as usual in Debian Med
packages
* Prevent autopkgtest on s390x since the package is no built here
* Standards-Version: 4.6.2 (routine-update)
-- Andreas Tille <tille@debian.org> Tue, 17 Jan 2023 16:15:35 +0100
bowtie2 (2.5.0-2) unstable; urgency=medium
* Package does not build on s390x any more
-- Andreas Tille <tille@debian.org> Mon, 12 Dec 2022 15:02:31 +0100
bowtie2 (2.5.0-1) unstable; urgency=medium
* Team upload.
[ Andreas Tille ]
* No salsa-ci for i386
* Use proper download file name
* New upstream version
* Standards-Version: 4.6.1 (routine-update)
* Use secure URI in Homepage field.
* Set upstream metadata fields: Bug-Database.
* Update patches
[ Étienne Mollier ]
* simde patch: adjust to introduction of AVX2 support.
* d/control: add pandoc to build doc/manual.html.
* d/rules: trigger refresh of the doc/manual.html.
* d/s/lintian-overrides: override missing source on doc/manual.html.
-- Étienne Mollier <emollier@debian.org> Sat, 05 Nov 2022 20:25:56 +0100
bowtie2 (2.4.5-1) unstable; urgency=medium
* New upstream version
* Drop transition for old debug package migration.
-- Andreas Tille <tille@debian.org> Thu, 17 Feb 2022 16:46:58 +0100
bowtie2 (2.4.4-1) unstable; urgency=medium
* Team upload.
* Fix watchfile to detect new versions on github (routine-update)
* Standards-Version: 4.6.0 (routine-update)
* Refresh patches
-- Michael R. Crusoe <crusoe@debian.org> Mon, 13 Sep 2021 18:45:11 +0200
bowtie2 (2.4.2-2) unstable; urgency=medium
[ Vagrant Cascadian ]
* Patch Makefile to set date for BUILD_TIME using SOURCE_DATE_EPOCH.
Closes: #977435
* Force same hostname to enable reproducible builds
Closes: #977436
[ Andreas Tille ]
* Standards-Version: 4.5.1 (routine-update)
* debhelper-compat 13 (routine-update)
* use binaries installed to debian/tmp
-- Andreas Tille <tille@debian.org> Tue, 15 Dec 2020 21:07:56 +0100
bowtie2 (2.4.2-1) unstable; urgency=medium
* New upstream version 2.4.2
* Refresh patches,
drop applied by upstream gcc10_ftbfs_invalid_dquote_char.patch
* Apply cme fix dpkg, drop version from libsimde-dev
-- Alexandre Mestiashvili <mestia@debian.org> Wed, 07 Oct 2020 20:06:52 +0200
bowtie2 (2.4.1-6) unstable; urgency=medium
* Team upload.
* Bump version requirement for libsimde-dev to grab ppc64el fixes.
-- Michael R. Crusoe <crusoe@debian.org> Mon, 01 Jun 2020 15:40:38 +0200
bowtie2 (2.4.1-5) unstable; urgency=medium
* Reproducible builds: filter out -ffile-prefix-map
Closes: #961494
-- Andreas Tille <tille@debian.org> Mon, 25 May 2020 14:14:23 +0200
bowtie2 (2.4.1-4) unstable; urgency=medium
* Team upload.
* Switch to libsimde-dev package from our code copy
-- Michael R. Crusoe <michael.crusoe@gmail.com> Tue, 21 Apr 2020 15:35:11 +0200
bowtie2 (2.4.1-3) UNRELEASED; urgency=medium
* Team upload.
* Add salsa-ci file (routine-update)
-- Michael R. Crusoe <michael.crusoe@gmail.com> Mon, 20 Apr 2020 17:54:38 +0200
bowtie2 (2.4.1-2) unstable; urgency=medium
* Add patch fixing FTBFS with gcc10, thanks to Jun Aruga
Closes: #957054
-- Alexandre Mestiashvili <mestia@debian.org> Sun, 19 Apr 2020 11:11:42 +0200
bowtie2 (2.4.1-1) unstable; urgency=medium
* Team upload.
* debian/control: not ready for 32-bit archs, and those builds often take
2-3+ hours to fail, so lets be nice and skip them.
Patches to fix 32-bit archs are very welcomed!
* Standards-Version: 4.5.0 (routine-update)
* Freshen patches
* debian/upstream/metadata: Add Bug-{Database,Submit},Repository{,-Browse}
* Update SIMDe version to 2a9ff6ddabfb940bdd29a0a0cd1ae3190f5fc97b 2020-04-03
-- Michael R. Crusoe <michael.crusoe@gmail.com> Sun, 01 Mar 2020 11:30:50 +0100
bowtie2 (2.3.5.1-6) unstable; urgency=medium
* Team upload.
* Remove the -m64 flag; not needed and not as universal as I thought
* This means we build on arm64. (Closes: #925499)
-- Michael R. Crusoe <michael.crusoe@gmail.com> Wed, 18 Dec 2019 13:36:56 +0100
bowtie2 (2.3.5.1-5) unstable; urgency=medium
* Team upload.
* debian/rules: Remove -santized here as well
-- Michael R. Crusoe <michael.crusoe@gmail.com> Wed, 18 Dec 2019 12:15:28 +0100
bowtie2 (2.3.5.1-4) unstable; urgency=medium
* Team upload.
* Added patch to correct the 64bit detection logic.
* Disable -fsanitize builds to save resources
-- Michael R. Crusoe <michael.crusoe@gmail.com> Mon, 16 Dec 2019 10:13:27 +0100
bowtie2 (2.3.5.1-3) unstable; urgency=medium
* Team upload.
* Enable all architectures via simde.
* Unset M64_FLAG and POPCNT_CAPABILITY on non AMD64 archs.
* debian/rules: Fix testing in with cowdancer or eatmydata by unsetting
LD_PRELOAD (the address sanitizer must be first in the library list)
* Added missing ${perl:Depends} for the bowtie2 binary package
-- Michael R. Crusoe <michael.crusoe@gmail.com> Sat, 14 Dec 2019 13:42:14 +0100
bowtie2 (2.3.5.1-2) unstable; urgency=medium
[ Steffen Möller ]
* Added ref to conda
[ Andreas Tille ]
* SEQwiki is deprecated
[ Steffen Moeller ]
* d/u/metadata: yamllint
[ Alexandre Mestiashvili ]
* Update d/patches/2to3.patch, use importlib instead of deprecated imp module
Closes: #945422
* Add patch silencing TBB deprecation warnings
* d/control: bump Policy to 4.4.1, add Rules-requires-root: no
-- Alexandre Mestiashvili <mestia@debian.org> Fri, 06 Dec 2019 22:38:21 +0100
bowtie2 (2.3.5.1-1) unstable; urgency=medium
[ Michael R. Crusoe ]
* bowtie-examples: set Multi-Arch: foreign
[ Steffen Moeller ]
* debhelper-compat 12
* Standards-Version: 4.4.0
* New upstream version - yet fails to build -> crash
[ Andreas Tille ]
* Use 2to3 to port to Python3
Closes: #936233
* Remove obsolete fields Name, Contact from debian/upstream/metadata.
* Build-Depends: libfile-which-perl
* (Build-)Depends: s/python/python3/
-- Alexandre Mestiashvili <mestia@debian.org> Thu, 05 Sep 2019 15:45:04 +0200
bowtie2 (2.3.4.3-1) unstable; urgency=medium
[ Steffen Möller ]
* Updated OMICtools ref in d/u/metadata
[ Alexandre Mestiashvili ]
* New upstream version 2.3.4.3:
- Fixed an issue causing `bowtie2-build` and `bowtie2-inspect`
to output incomplete help text.
- Fixed an issue causing `bowtie2-inspect` to crash.
- Fixed an issue preventing `bowtie2` from processing paired and/or
unpaired FASTQ reads together with interleaved FASTQ reads.
* Bump Policy to 4.2.1
-- Alexandre Mestiashvili <mestia@debian.org> Tue, 25 Sep 2018 07:58:26 +0000
bowtie2 (2.3.4.2-1) unstable; urgency=medium
* New upstream version 2.3.4.2
* Bump Standards-Version to 4.2.0
* Refresh patches
* Add patch fixing interpreter for bowite2 scripts
* Add patch removing reference to js lib for ie...
* Update uploader's email
-- Alexandre Mestiashvili <mestia@debian.org> Tue, 14 Aug 2018 13:31:56 +0200
bowtie2 (2.3.4.1-2) unstable; urgency=medium
* Team upload.
* Autopkgtest: add test that checks correct program behaviour when it called
without arguments
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.4
-- Liubov Chuprikova <chuprikovalv@gmail.com> Tue, 12 Jun 2018 15:15:38 +0200
bowtie2 (2.3.4.1-1) unstable; urgency=medium
* New upstream version 2.3.4.1
* Refresh d/patches/reproducible.patch
* Check DEB_BUILD_PROFILES against nocheck, strip trailing white spaces
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Wed, 07 Feb 2018 23:23:01 +0100
bowtie2 (2.3.4-1) unstable; urgency=medium
* New upstream version 2.3.4
* Refresh patches
* Update d/rules, add sanitized binaries for tests
* Update d/bowties2.docs
* Use /usr/share/dpkg/architecture.mk to find DEB_HOST_ARCH
* Bump Standards-Version: to 4.1.3, debhelper and compatibility level to 11
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Sat, 06 Jan 2018 15:45:55 +0100
bowtie2 (2.3.3.1-1) unstable; urgency=medium
* Update Files-Excluded list in d/copyright
* Bump Standards-Version to 4.1.1
* New upstream version 2.3.3.1
* Refresh patches
* Don't run random-test at all as it depends on non-free Math::Random package
* Drop single-cpu-for-test.patch, as we disabled random-test target completely
* Remove unnecessary testsuite line from d/control
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Fri, 13 Oct 2017 15:14:20 +0200
bowtie2 (2.3.3-1) unstable; urgency=medium
[ Steffen Moeller ]
* debian/upstream/metadata: Corrected syntax
* debian/control: policy bump to 4.0.1
[ Alexandre Mestiashvili ]
* Update Files-Excluded section in d/copyright
* New upstream version 2.3.3
* Bump Standards-Version in d/control
* Refresh patches
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Mon, 11 Sep 2017 12:50:49 +0200
bowtie2 (2.3.2-2) unstable; urgency=medium
[ Steffen Moeller ]
* Added RRID (SCR_005476)
* Added OMICtools ref (OMIC_00653)
[ matuskalas ]
* Added bio.tools ref and removed whole URLs (@smoe decision)
[ Alexandre Mestiashvili ]
* Bump Standards-Version to 4.0.0
* Hardcode binary package name instead of using dpkg-parsechangelog
* Upload to unstable
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Thu, 27 Jul 2017 15:30:16 +0200
bowtie2 (2.3.2-1) experimental; urgency=medium
* New upstream version 2.3.2
* Drop libreadline-dev build dependency
* Refresh patches
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Wed, 24 May 2017 10:33:13 +0200
bowtie2 (2.3.1-1) unstable; urgency=medium
* New upstream version 2.3.1
* Refresh patches
* Add zlib1g-dev and libreadline-dev build dependencies
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Tue, 07 Mar 2017 11:10:09 +0100
bowtie2 (2.3.0-2) unstable; urgency=medium
* Team upload.
[ Sascha Steinbiss ]
* Skip tests involving simulated reads to avoid use of non-free build-dep
libmath-random-perl again.
Closes: #852546
* Add libclone-perl build dependency.
[ Alexandre Mestiashvili ]
* Add patch suppressing -Wmisleading-indentation warnings.
[ Steffen Moeller ]
* Adjust EDAM annotations.
-- Sascha Steinbiss <satta@debian.org> Wed, 25 Jan 2017 16:27:13 +0100
bowtie2 (2.3.0-1) unstable; urgency=medium
* Team upload.
[ Andreas Tille ]
* New upstream version
* Code available on Github
* debhelper 10
* Remove Carlos Borroto from Uploaders
* Remove code from test suite that is requiring non-free package
libmath-random-perl
* New Build-Depends to run build time test: liblocal-lib-perl
[ Sascha Steinbiss ]
* Even more new Build-Depends: libmath-random-perl, libtest-deep-perl
* Disable rebuilding during tests
-- Sascha Steinbiss <satta@debian.org> Sat, 14 Jan 2017 07:50:51 +0000
bowtie2 (2.2.9-4) unstable; urgency=medium
* Team upload.
* Make build reproducible by adding compiler flags
setting -fdebug-prefix-map.
-- Sascha Steinbiss <satta@debian.org> Thu, 25 Aug 2016 12:47:33 +0000
bowtie2 (2.2.9-3) unstable; urgency=medium
* Team upload.
* Fix building with GCC 6.
Closes: #831157.
-- Sascha Steinbiss <satta@debian.org> Sat, 16 Jul 2016 03:22:51 +0000
bowtie2 (2.2.9-2) unstable; urgency=medium
* Team upload.
* Make build reproducible.
- Remove embedding of build hostname, time and compiler.
- Fix help2man wrapper heredoc.
- Sort wildcard expansions in Makefile.
- Pin down language settings.
-- Sascha Steinbiss <sascha@steinbiss.name> Sat, 21 May 2016 17:18:25 +0000
bowtie2 (2.2.9-1) unstable; urgency=medium
* Imported Upstream version 2.2.9
* Bump Standards-Version
* Revert the commit with applied patch
* Update hardening.patch
* Cleanup d/rules, remove CPPFLAGS as they are imported anyway
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Thu, 28 Apr 2016 09:26:48 +0200
bowtie2 (2.2.8-1) unstable; urgency=medium
[ Andreas Tille ]
* New upstream version repackaged as xz
* cme fix dpkg-control
[ Alexandre Mestiashvili ]
* Imported Upstream version 2.2.8
* d/rules: export DEB_BUILD_MAINT_OPTIONS = hardening=+all
* d/copyright: Merge Files: stanzas and update years
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Sat, 12 Mar 2016 15:57:34 +0100
bowtie2 (2.2.6-2) unstable; urgency=medium
[ Charles Plessy ]
* d/rules: quote variables contents passed to Makefile, closes: #809076.
-- Andreas Tille <tille@debian.org> Mon, 28 Dec 2015 08:23:51 +0100
bowtie2 (2.2.6-1) unstable; urgency=medium
* Imported Upstream version 2.2.6
* d/rules: WITH_TBB=1
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Fri, 28 Aug 2015 09:31:45 +0200
bowtie2 (2.2.5-2) unstable; urgency=medium
* Upload to unstable
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Tue, 28 Apr 2015 18:06:34 +0200
bowtie2 (2.2.5-1) experimental; urgency=medium
* Imported Upstream version 2.2.5
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Wed, 18 Mar 2015 10:09:35 +0100
bowtie2 (2.2.4-2) unstable; urgency=medium
* d/control: add python dependency, needed to build bowtie2-build man page
Closes: #769934
* d/watch: fix upstream url parsing, see #766878
* d/rules: remove byte-compiled bowtie2-buildc
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Tue, 18 Nov 2014 23:28:33 +0100
bowtie2 (2.2.4-1) unstable; urgency=medium
[ Andreas Tille ]
* d/control: Priority: optional
* add missing DEP3 description
[ Alexandre Mestiashvili ]
* d/test/binary-run: test that binary work
* d/test/control: add binary-run
[ Andreas Tille ]
* New upstream version
* do uscan call directly in debian/rules instead of separate script
* cme fix dpkg-control
-- Andreas Tille <tille@debian.org> Sun, 26 Oct 2014 07:08:46 +0100
bowtie2 (2.2.3-1) unstable; urgency=medium
* Imported Upstream version 2.2.3
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Tue, 03 Jun 2014 16:13:47 +0200
bowtie2 (2.2.2-1) unstable; urgency=medium
* Imported Upstream version 2.2.2
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Tue, 15 Apr 2014 13:40:01 +0200
bowtie2 (2.2.1-1) unstable; urgency=medium
* Imported Upstream version 2.2.1
* d/changelog: updated Copyright years
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Fri, 07 Mar 2014 09:37:13 +0100
bowtie2 (2.2.0-1) unstable; urgency=medium
[ Alexandre Mestiashvili ]
* Imported Upstream version 2.2.0
[ James McCoy ]
* Move debian/upstream to debian/upstream/metadata
[ Alexandre Mestiashvili ]
* refreshed patches, dropped fix_makefile_machine_detection.patch
* d/control: bump Standards-Version
Architecture: amd64 kfreebsd-amd64, starting from this version
bowtie2 works on amd64 only
added python to Depends:
* d/rules: remove i386 related fixes,rules for new binaries
* d/bowtie2.install: added new binaries introduced by the new version
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Thu, 20 Feb 2014 13:29:58 +0100
bowtie2 (2.1.0-2) unstable; urgency=low
* Closes: #713000
* d/control: fixed description for bowtie2-examples,
bumped Standards-Version,
removed DM-Upload-Allowed,
use canonical vcs
* d/tests/: underscore are not allowed for tests
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Tue, 25 Jun 2013 13:58:18 +0200
bowtie2 (2.1.0-1) unstable; urgency=low
* - d/help2man-wrapper: as kindly suggested by Andreas Tille
Closes: #701686
- d/rules: use help2man-wrapper instead of help2man to generate man pages
* Imported Upstream version 2.1.0
* refreshed patches
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Wed, 27 Feb 2013 15:58:40 +0100
bowtie2 (2.0.6-1) unstable; urgency=low
* Imported Upstream version 2.0.6
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Tue, 19 Feb 2013 17:30:42 +0100
bowtie2 (2.0.5-1) unstable; urgency=low
* Imported Upstream version 2.0.5
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Fri, 11 Jan 2013 11:19:34 +0100
bowtie2 (2.0.4-1) unstable; urgency=low
* Imported Upstream version 2.0.4
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Thu, 27 Dec 2012 17:33:36 +0100
bowtie2 (2.0.2-1) unstable; urgency=low
[ Carlos Borroto ]
* Imported Upstream version 2.0.2
* bowtie2_gcc4.7.patch no longer needed
[ Alexandre Mestiashvili ]
* added autopkgtest testsuite
* updated Uploaders field
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Mon, 19 Nov 2012 16:31:02 +0100
bowtie2 (2.0.0-beta7-1) unstable; urgency=low
[ Alexandre Mestiashvili ]
* debian/control force architcures to i386/amd64 kfreebsd-i386/amd64 and
hurd-i386 SSE is not availbale on others. Closes: #668123
* debhelper version 9
* debian/rules forced hardening flags
* hardening.patch to inject hardening CPPFLAGS
* Imported Upstream version 2.0.0-beta7
* debian/bowtie2.lintian-overrides to avoid lintian's waring
to be fixed by using epochs and tilda in upstream version
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Mon, 30 Jul 2012 13:51:31 +0200
bowtie2 (2.0.0-beta6-3) unstable; urgency=low
* normalized architecture detection.
For example kfreebsd-amd64 is detected as an amd64 architecture
and msse flag is set.(Previous commit was wrong) (Closes: #673159)
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Fri, 01 Jun 2012 21:58:49 +0200
bowtie2 (2.0.0-beta6-2) unstable; urgency=low
* debian/rules normalized output of dpkg-architecture,
so for example kfreebsd-amd64 is detected as an amd64 architecture
and sse flags are enabled for it.
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Thu, 31 May 2012 19:22:56 +0200
bowtie2 (2.0.0-beta6-1) unstable; urgency=low
* updated debian/watch and get-orig-source to track -source suffix
* Imported Upstream version 2.0.0-beta6
* debian/patches/fix_makefile_machine_detection.patch
use -msse2 only for Intel architectures, Closes: #672526
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Fri, 11 May 2012 08:41:59 +0200
bowtie2 (2.0.0-beta5-2) unstable; urgency=low
[ Alexandre Mestiashvili ]
* file sse_util.h has missing copyright header.
The Author (Benjamin Langmead) has
confirmed that the file is distributed under GPL3 license.
[ Andreas Tille ]
* debian/upstream: Added publication
* debian/patches/fix_makefile_machine_detection.patch + debian/rules:
prevent -mXX and -msse2 switches for non Intel architectures
[ Alexandre Mestiashvili ]
* debian/patches/bowtie2_gcc4.7.patch Closes: #672090
* updated DEP3 headers
* bumperd Standards-Version to 3.9.3
* uname -m doesn't detect 32 bit chroot env - updated patcH
-- Andreas Tille <tille@debian.org> Thu, 26 Apr 2012 13:59:54 +0200
bowtie2 (2.0.0-beta5-1) unstable; urgency=low
[ Alexandre Mestiashvili ]
* Initial release (Closes: #660762)
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Wed, 22 Feb 2012 11:03:03 +0100