bioperl-run (1.7.3-6) unstable; urgency=medium
* Team upload.
* d/control: restrict build-dependencies to their supported architectures.
* added skip-test-for-kalign.patch
-- Étienne Mollier <etienne.mollier@mailoo.org> Wed, 06 Jan 2021 22:38:23 +0100
bioperl-run (1.7.3-5) unstable; urgency=medium
* Team upload.
[ Michael R. Crusoe ]
* Add build-dep on libfile-sort-perl as that has arrived in Debian
* debian/upstream/metadata: Add Repository & Repository-Browse
[ Pranav Ballaney ]
* Disable tests for RemoteBlast
* Disable tests for RemoteBlast_rpsblast
* Extract BEDTools version properly
[ Andreas Tille ]
* Depends: libfile-sort-perl
Closes: #974168
* Standards-Version: 4.5.1 (routine-update)
* debhelper-compat 13 (routine-update)
* Remove trailing whitespace in debian/control (routine-update)
[ Étienne Mollier ]
* Add get-overlap.patch to map to the proper "getOverlap" wrapper.
* Add build time test dependencies to get BEDtools test data sets.
* Add alternate-data.patch to use a dataset available in the Debian
archive during build time testings.
* Suppress retries when attempting to access remote Blast resources,
this prevents hogging autopkgtest runners ten more minutes.
-- Étienne Mollier <etienne.mollier@mailoo.org> Thu, 03 Dec 2020 21:57:37 +0100
bioperl-run (1.7.3-4) unstable; urgency=medium
[ Michael R. Crusoe ]
* Team upload.
* Fix the autopkgtests
* Set 'Bio::Factory::EMBOSS' as the main module name for the purpose of
the use.t autopkgtest
* fix hyphympi autopkgtests
* libipc-run-perl is needed for Bio::Tools::Run::BEDTools
* drawgram is pary of the phylip package
[ Pranav Ballaney ]
* Change kalign command string to input via stdin It fails to take input
via the -in flag during testing
* Revert changes made outside of debian/
* Update quilt version
* Kalign takes input via a pipe
* Extract Kalign version properly (Closes: #954511)
[ Andreas Tille ]
* Standards-Version: 4.5.0 (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Wrap long lines in changelog entries: 1.7.2-1.
* Set upstream metadata fields: Bug-Submit.
-- Pranav Ballaney <ballaneypranav@gmail.com> Tue, 31 Mar 2020 01:13:25 +0530
bioperl-run (1.7.3-3) unstable; urgency=medium
* Team upload.
* Depends: libbio-tools-run-alignment-clustalw-perl (Closes: #948323)
* Depends: libbio-featureio-perl
-- Michael R. Crusoe <michael.crusoe@gmail.com> Tue, 07 Jan 2020 12:07:09 +0100
bioperl-run (1.7.3-2) unstable; urgency=medium
* Depends: libbio-tools-run-alignment-clustalw
* Build-Depends / Recommends: s/blast2/ncbi-blast+-legacy/
Closes: #948082
* debhelper-compat 12
* Standards-Version: 4.4.1
* Remove trailing whitespace in debian/changelog
* Remove trailing whitespace in debian/copyright
* Set upstream metadata fields: Bug-Database.
-- Andreas Tille <tille@debian.org> Sat, 04 Jan 2020 17:49:32 +0100
bioperl-run (1.7.3-1) unstable; urgency=medium
* New upstream version
* debhelper 12
* Standards-Version: 4.3.0
* Drop dependencies: bowtie, bwa, maq, t-coffee, gmap, paml
Thanks for the hint to Carnë Draug <carandraug+dev@gmail.com>)
* Versioned (Build-)Depends: bioperl (>= 1.7.4)
-- Andreas Tille <tille@debian.org> Mon, 11 Feb 2019 22:14:53 +0100
bioperl-run (1.7.2-4) unstable; urgency=medium
* (Build-)Depends: ncoils
* do not run tests parallel to get sensibly sorted output
* Allow MPI oversubscription (as in phyml build since phyml caused
problems inside build time tests)
This is also not reliable - skip phyml test at all
Closes: #906337
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
* Fix Homepage
* Lintian-override for script-with-language-extension
-- Andreas Tille <tille@debian.org> Fri, 14 Sep 2018 20:10:08 +0200
bioperl-run (1.7.2-3) unstable; urgency=medium
* Drop adjust_bowtie_tests.patch, Closes: #887578
* Bump Standards-Version to 4.1.3 (no changes needed)
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Fri, 26 Jan 2018 10:43:45 +0100
bioperl-run (1.7.2-2) unstable; urgency=medium
* Team upload
* Add adjust_bowtie_tests.patch fixing failing tests for Bowtie
Closes: #880347
* Bump Standards-Version to 4.1.2, apply cme fix dpkg
-- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Thu, 07 Dec 2017 18:19:04 +0100
bioperl-run (1.7.2-1) unstable; urgency=medium
* New upstream version
* Convert packaging from SVN to Git
* For some reason Ensembl.t test is executed in autopkgtest run even if it
should be skipped due to missing preconditions
(http://search.cpan.org/~cjfields/Bio-EUtilities-1.72/lib/Bio/DB/EUtilities.pm)
The test will now be fully removed to make sure it is skipped.
* Standards-Version: 4.1.0 (no changes needed)
* Do not try to run bowtie tests with wrong bowtie call
Closes: #868073
-- Andreas Tille <tille@debian.org> Wed, 20 Sep 2017 14:29:45 +0200
bioperl-run (1.7.1-3) unstable; urgency=medium
* s/Conflicts/Breaks/
Closes: #850029
-- Andreas Tille <tille@debian.org> Fri, 13 Jan 2017 08:25:26 +0100
bioperl-run (1.7.1-2) unstable; urgency=medium
* Conflicts: libbio-perl-perl (<< 1.7.1-1)
Closes: #850029
-- Andreas Tille <tille@debian.org> Tue, 03 Jan 2017 21:10:54 +0100
bioperl-run (1.7.1-1) unstable; urgency=medium
* New upstream version
* Testsuite: autopkgtest-pkg-perl
* cme fix dpkg-control
* Enable lots of tests
* Module Bio::Tools::Run::WrapperBase was taken over from BioPerl into
bioperl-run in commit acd57a7d14112c5fd2cd979005b072efdaf57679 which is
taken over in quilt patch
* Fix homepage
* d/watch:
- version=4
- Fix versionmangling
* Build-Depends: raxml
* Update copyright
* debhelper 10
-- Andreas Tille <tille@debian.org> Wed, 21 Dec 2016 21:24:05 +0100
bioperl-run (1.6.9-3) unstable; urgency=medium
[ Charles Plessy ]
* Build-depend on libmodule-build-perl, Closes: #788888.
[ Andreas Tille ]
* Compliant with Standards-Version: 3.9.6
-- Charles Plessy <plessy@debian.org> Tue, 23 Jun 2015 20:05:10 +0900
bioperl-run (1.6.9-2) unstable; urgency=low
* debian/source/format: 3.0 (quilt)
* debian/control:
- cme fix dpkg-control
- canonical Vcs URLs
- debhelper 9
* debian/README.source: removed because redundant
* debian/copyright: DEP5
* debian/watch: Point download location to github which provides more
reliable version numbering than CPAN which would have needed a more
complex version mangling
* refreshed quilt patches to get rid of fuzz
-- Andreas Tille <tille@debian.org> Fri, 15 Nov 2013 10:03:29 +0100
bioperl-run (1.6.9-1) unstable; urgency=low
* New upstream release.
* Converted and validated debian/copyright to latest machine-readable format.
* debian/control:
- Refreshed the list of packages for which wrappers are provided, in the
Suggests field as well as in an experimental Build-Recommends field.
- Incremented Standards-Version to reflect conformance with Policy 3.9.2.
No other changes needed.
- Vcs-Browser URL made redirectable to viewvc.
- Removed useless ‘svn’ in the Vcs-Svn URL.
* Point debian/watch to CPAN.
* Tiny style with Debhelper 8 (debian/rules, debian/compat, debian/control).
* Split scripts in bioperl-run and modules in libbio-perl-run-perl.
(debian/rules, debian/control, debian/bioperl-run.install,
debian/libbio-perl-run-perl.install)
* debian/rules, debian/patches/series, debian/control:
- debian/patches/install-scripts.patch for non-interactive script install.
- debian/patches/Use-system-s-Perl.patch against /usr/local/bin/perl.
- debian/patches/Some-spellchecking.patch.
* Trigger network tests with DEB_MAINTAINER_MODE (debian/rules,
debian/README.test).
-- Charles Plessy <plessy@debian.org> Sat, 18 Jun 2011 13:21:36 +0900
bioperl-run (1.6.1-1) unstable; urgency=low
* New upstream release.
* debian/patches/10-wrong-path-for-interpreter.patch: removed
(fixed upstream).
* debian/watch updated (bioperl -> BioPerl).
* debian/rules refreshed with dh-make-perl 0.53.
- Disabled installation of examples (removed upstream).
- Removed the correction of file permission of Pise documentation
(removed upstream).
- Removed patching facilities (no patches anymore).
- Disabled tests as I experience failures with t/Eponine.t despite
this program is not installed.
* debian/copyright:
- Removed vanity lines about debianization and debian copyright.
- Incremented years to 2009.
- Updated to latest experimentation of the machine-readable license summary.
* debian/control:
- Incremented Standards-Version to reflect conformance on new Policy
(dropped versionned build-dependancy on Perl).
- Removed build-dependancy on quilt (no patches anymore).
- Depend and Build-Depend on bioperl versions superior or equal to 1.6.0.
- Build-depends on, and Recommdnes libalgorithm-diff-perl, libipc-run-perl,
libio-string-perl and libxml-twig-perl, that are listed in DEPENDANCIES.
- Build-depends on libarray-compare-perl and libtree-dagnode-perl
(otherwise tests fail).
- Depend on amap-align instead of amap (Closes: #541274).
-- Charles Plessy <plessy@debian.org> Thu, 03 Sep 2009 11:00:03 +0900
bioperl-run (1.5.2.100-1) unstable; urgency=low
* Initial Release (Closes: #505112).
-- Charles Plessy <plessy@debian.org> Mon, 10 Nov 2008 09:11:17 +0900