bowtie2 (2.5.4-1) unstable; urgency=medium * Remove libmath-random-perl from Test-Depends and complete patch removing tests needing this module Closes: #1078087 * New upstream version * Standards-Version: 4.7.0 (routine-update) -- Andreas Tille Wed, 07 Aug 2024 13:31:40 +0200 bowtie2 (2.5.3-1) unstable; urgency=medium [ Michael R. Crusoe ] * Team upload. * d/control: simplify architecture specifications by using provisions from the architecture-properties package. -- Charles Plessy Wed, 17 Apr 2024 08:56:57 +0900 bowtie2 (2.5.2-1) unstable; urgency=medium * New upstream version * Add build support for loongarch64 Closes: #1059510 -- Andreas Tille Wed, 10 Jan 2024 20:37:29 +0100 bowtie2 (2.5.1-1) unstable; urgency=medium * Team upload. * New upstream version * refresh patches. * d/patches: update my email address, add some Forwarded hints * tests: remove need to build debug versions. * d/tests: run built-in tests as well. -- Michael R. Crusoe Tue, 12 Sep 2023 13:16:13 +0200 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Fri, 28 Aug 2015 09:31:45 +0200 bowtie2 (2.2.5-2) unstable; urgency=medium * Upload to unstable -- Alexandre Mestiashvili Tue, 28 Apr 2015 18:06:34 +0200 bowtie2 (2.2.5-1) experimental; urgency=medium * Imported Upstream version 2.2.5 -- Alexandre Mestiashvili 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 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 Sun, 26 Oct 2014 07:08:46 +0100 bowtie2 (2.2.3-1) unstable; urgency=medium * Imported Upstream version 2.2.3 -- Alexandre Mestiashvili Tue, 03 Jun 2014 16:13:47 +0200 bowtie2 (2.2.2-1) unstable; urgency=medium * Imported Upstream version 2.2.2 -- Alexandre Mestiashvili 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 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 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 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 Wed, 27 Feb 2013 15:58:40 +0100 bowtie2 (2.0.6-1) unstable; urgency=low * Imported Upstream version 2.0.6 -- Alexandre Mestiashvili Tue, 19 Feb 2013 17:30:42 +0100 bowtie2 (2.0.5-1) unstable; urgency=low * Imported Upstream version 2.0.5 -- Alexandre Mestiashvili Fri, 11 Jan 2013 11:19:34 +0100 bowtie2 (2.0.4-1) unstable; urgency=low * Imported Upstream version 2.0.4 -- Alexandre Mestiashvili 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 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 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 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 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 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 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 Wed, 22 Feb 2012 11:03:03 +0100