debian/0000755000000000000000000000000012227347105007171 5ustar debian/rules0000755000000000000000000000175012047044152010250 0ustar #!/usr/bin/make -f # -*- makefile -*- # Build rules for the Debian package mafft. # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 %: dh $@ override_dh_auto_build: $(MAKE) -C core PREFIX=/usr/lib/mafft ENABLE_MULTITHREAD=-Denablemultithread LIBDIR=/usr/lib/mafft/lib/mafft CFLAGS="$(shell dpkg-buildflags --get CFLAGS)" CPPFLAGS="$(shell dpkg-buildflags --get CPPFLAGS)" CXXFLAGS="$(shell dpkg-buildflags --get CXXFLAGS)" LDFLAGS="$(shell dpkg-buildflags --get LDFLAGS)" override_dh_clean: [ ! -f core/Makefile ] || $(MAKE) -C core clean rm -rf binaries/* scripts/* dh_clean MAFFT = MAFFT_BINARIES=$(CURDIR)/binaries scripts/mafft override_dh_install: $(MAKE) -C core PREFIX=$(CURDIR)/debian/mafft/usr/lib/mafft MANDIR=$(CURDIR)/debian/mafft/usr/share/man/man1 LIBDIR=$(CURDIR)/debian/mafft/usr/lib/mafft/lib/mafft install rm $(CURDIR)/debian/mafft/usr/lib/mafft/lib/mafft/*.1 override_dh_compress: dh_compress -X test/sample override_dh_builddeb: dh_builddeb -- -Z xz debian/source/0000755000000000000000000000000012227347105010471 5ustar debian/source/format0000644000000000000000000000001411410643755011702 0ustar 3.0 (quilt) debian/copyright0000644000000000000000000000365112227347067011140 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://mafft.cbrc.jp/alignment/software/mafft-7.123-without-extensions-src.tgz Comment: Debian only distributes MAFFT without its extensions. The mafft-*-with-extensions-src.tgz upstream packages have an ‘extensions’ directory, which contains code from the Vienna RNA package, that does not allow commercial use and is therefore unsuitable for Debian. Files: * Copyright: © 2009-2012 Kazutaka Katoh License: mafft Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. . The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Files: debian/* Copyright: (C) 2009 Andreas Tille License: same-as-mafft See above debian/tests/0000755000000000000000000000000012227347105010333 5ustar debian/tests/with-example-data0000644000000000000000000000117112226644370013574 0ustar #!/bin/sh -e MAFFT="mafft --thread 0" TESTDATADIR=/usr/share/doc/mafft/test/ $MAFFT $TESTDATADIR/sample | diff $TESTDATADIR/sample.fftns2 - $MAFFT --maxiterate 100 $TESTDATADIR/sample | diff $TESTDATADIR/sample.fftnsi - $MAFFT --globalpair $TESTDATADIR/sample | diff $TESTDATADIR/sample.gins1 - $MAFFT --globalpair --maxiterate 100 $TESTDATADIR/sample | diff $TESTDATADIR/sample.ginsi - $MAFFT --localpair $TESTDATADIR/sample | diff $TESTDATADIR/sample.lins1 - $MAFFT --localpair --maxiterate 100 $TESTDATADIR/sample | diff $TESTDATADIR/sample.linsi - debian/tests/control0000644000000000000000000000003112036455420011726 0ustar Tests: with-example-data debian/docs0000644000000000000000000000000511260116524010032 0ustar test debian/watch0000644000000000000000000000014412226627630010224 0ustar version=3 http://mafft.cbrc.jp/alignment/software/source.html mafft-(.*)-without-extensions-src.tgz debian/links0000644000000000000000000000172311536532743010245 0ustar usr/share/man/man1/mafft.1 usr/share/man/man1/mafft-linsi.1 usr/share/man/man1/mafft.1 usr/share/man/man1/mafft-ginsi.1 usr/share/man/man1/mafft.1 usr/share/man/man1/mafft-einsi.1 usr/share/man/man1/mafft.1 usr/share/man/man1/mafft-fftnsi.1 usr/share/man/man1/mafft.1 usr/share/man/man1/mafft-fftns.1 usr/share/man/man1/mafft.1 usr/share/man/man1/linsi.1 usr/share/man/man1/mafft.1 usr/share/man/man1/ginsi.1 usr/share/man/man1/mafft.1 usr/share/man/man1/einsi.1 usr/share/man/man1/mafft.1 usr/share/man/man1/fftnsi.1 usr/share/man/man1/mafft.1 usr/share/man/man1/fftns.1 usr/share/man/man1/mafft.1 usr/share/man/man1/mafft-profile.1 usr/lib/mafft/bin/mafft-homologs.rb usr/bin/mafft-homologs usr/lib/mafft/bin/mafft usr/bin/mafft # override broken symlinks created in Makefile usr/lib/mafft/lib/mafft/mafft-distance usr/lib/mafft/bin/mafft-distance usr/lib/mafft/lib/mafft/mafft-profile usr/lib/mafft/bin/mafft-profile debian/changelog0000644000000000000000000001530112227347056011050 0ustar mafft (7.123-1) unstable; urgency=low * New upstream version. * Correct watch file, which was downloading the non-free version. This error did not affect the current stable release of Debian. * debian/tests/with-example-data: disable multithreading to stabilise output. -- Charles Plessy Wed, 16 Oct 2013 08:22:20 +0900 mafft (7.058-1) unstable; urgency=low * New upstream version incorporated debian/patches Closes: #715827, #715830, #715831, #715847, #715881 -- Andreas Tille Sun, 04 Aug 2013 08:51:10 +0200 mafft (7.055-1) unstable; urgency=low [ Charles Plessy ] * Signal the use of autopkgtest in debian/control (closes: #692683). [ Andreas Tille ] * New upstream version * debian/README.source: removed because redundant * debian/patches/hardening.patch: Enable propagation of hardening options * debian/control: use anonscm in Vcs fields -- Andreas Tille Tue, 30 Jul 2013 13:39:43 +0200 mafft (6.940-1) unstable; urgency=low [ Charles Plessy ] * New upstream release (no new license nor copyright statement). * Removed unnecessary build-dependance on quilt. * Test for regressions with autopkgtest insted of doing it at build time. (debian/control, debian/tests/control, debian/tests/with-example-data) * debian/control: - Removed 'Pre-Depends: dpkg (>= 1.15.6)' now that Ubuntu LTS 12.04 is out. - Increment Standards-Version to show conformance with Policy 3.9.4. - Removed DM-Upload-Allowed field. - Normalised with the command cme fix dpkg-control. - Use Debhelper 9 (also debian/compat). * Pass dpkg build flags in debian/rules. [ Andreas Tille ] * debian/upstream: - Single Reference field instead of Reference-* - Add additional reference from tasks file - Authors in BibTeX conform format -- Charles Plessy Sun, 14 Oct 2012 15:42:54 +0900 mafft (6.864-1) unstable; urgency=low * New upstream release. * Pre-Depends on dpkg (>= 1.15.6) for xz compression support (debian/control). * Renamed debian/README.Debian debian/README.test. * Track the new website in debian/watch. -- Charles Plessy Thu, 12 Jan 2012 19:00:31 +0900 mafft (6.860-1) unstable; urgency=low * New upstream release. * Simplified debian/watch. * Updated Homepage (debian/control). * Compress binary package with xz (debian/control). -- Charles Plessy Sun, 18 Sep 2011 14:43:10 +0900 mafft (6.859-1) unstable; urgency=low * New upstream release. * Converted debian/copyright to machine-readable (DEP 5) format. -- Charles Plessy Sat, 27 Aug 2011 12:06:00 +0900 mafft (6.857-1) unstable; urgency=low * New upstream version. * Enable multithread, correct FHS path (debian/rules). * Removed extra manpage copies instead of patching Makefile and installing via debhleper (debian/patches, debian/rules, debian/manpages). * Removed debian/dirs, not needed anymore. * Run the tests after installation, and allow them to fail (debian/rules). * Build when running debian/rules build (override typo, Closes: #636634). * Corrected VCS fields in debian/control. * Incremented Standards-Version to reflect conformance wiht Policy 3.9.2 (debian/control, no changes needed). -- Charles Plessy Fri, 05 Aug 2011 09:54:09 +0900 mafft (6.850-1) unstable; urgency=low * New upstream version * Adapted patch to new upstream * Debhelper 8 (control + compat) * debian/rules: Switch to dh * debian/links: override broken symlinks created in Makefile -- Andreas Tille Sat, 12 Mar 2011 00:02:43 +0100 mafft (6.833-1) unstable; urgency=low * New upstream version -- Andreas Tille Wed, 17 Nov 2010 13:51:28 +0100 mafft (6.815-1) unstable; urgency=low * New upstream version * Switch to source format 3.0 (quilt) * Standards-Version: 3.9.1 (no changes needed) -- Andreas Tille Thu, 05 Aug 2010 10:29:50 +0200 mafft (6.811-1) unstable; urgency=low * New upstream version * Standards-Version: 3.8.4 (no changes needed) -- Andreas Tille Thu, 24 Jun 2010 13:08:06 +0200 mafft (6.717-1) unstable; urgency=low * New upstream version * Added a few informations about Upstream in debian/upstream-metadata.yaml. * Documented how this package is tested in debian/README.Debian. * Refreshed debian/copyright, using the verbatim upstream license, indented with a tabulation. -- Charles Plessy Mon, 14 Dec 2009 13:02:59 +0900 mafft (6.716-1) unstable; urgency=low * New upstream version -- Andreas Tille Tue, 03 Nov 2009 12:39:12 +0100 mafft (6.713-1) unstable; urgency=low [ David Paleino ] * debian/control: - removed myself from Uploaders [ Andreas Tille ] * New upstream version * debian/control: - Standards-Version: 3.8.3 (no changes needed) - s/Debian-Med/Debian Med/ - Recommends: blast2, lynx, ruby (instead of Suggests - we have a Ruby script in /usr/bin using blast and lynx. * debhelper 7 * No need for debian/patches/Securisation-by-mktemp-usage.patch any more * debian/watch: Handle -with.*-extensions naming - we are dealing with the without-extensions tarball in Debian -- Andreas Tille Mon, 28 Sep 2009 09:02:30 +0200 mafft (6.240-2) unstable; urgency=high [ Charles Plessy ] * debian/control: - Moved the Homepage: field out from the package's description. - Enhances: t-coffee. * Updated my email address. * Securisation of the temorary files of mafft-homologs: - debian/control: build-depend on quilt. - debian/rules: modified to use quilt. - debian/README.source: signals that the package uses quilt. - debian/patches: added a patch to use non-guessable temporary files (Closes: #496366). Thanks to Dmitry E. Oboukhov for finding the bug, Thijs Kinkhorst for preliminary, Kazutaka Katoh for the final implementation, and Michael Schutte for the final review. - debian/mafft-homologs.1*, debian/README.Debian: document that the program is patched. [ David Paleino ] * debian/mafft.1, debian/mafft-homologs.1 added - manpages built statically. * debian/control: - B-D updated (see above) - added myself to Uploaders - moved XS-Vcs-* fields to Vcs-* - Updated to Standards-Version 3.7.3 (no changes needed) * debian/rules: - reflecting static build of manpages - minor changes -- Charles Plessy Mon, 25 Aug 2008 23:30:20 +0900 mafft (6.240-1) unstable; urgency=low * Initial release (Closes: #409640) -- Charles Plessy Sat, 9 Jun 2007 12:06:43 +0900 debian/upstream0000644000000000000000000000173012226642416010757 0ustar Contact: Kazutaka Katoh Name: MAFFT Homepage: http://mafft.cbrc.jp/alignment/software/ Reference: - Author: Katoh, Kazutaka and Toh, Hiroyuki Title: Recent developments in the MAFFT multiple sequence alignment program Journal: Brief Bioinform Year: 2008 Volume: 9 Number: 4 Pages: 286-298 DOI: 10.1093/bib/bbn013 PMID: 18372315 URL: http://bib.oxfordjournals.org/cgi/content/abstract/9/4/286 - Author: K. Katoh and G. Asimenos and H. Toh Title: Multiple alignment of DNA sequences with MAFFT Journal: Methods Mol Biol. Volume: 537 Pages: 39-64 Year: 2009 PMID: 19378139 DOI: 10.1007/978-1-59745-251-9_3 URL: http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-251-9_3 eprint: http://www.springerprotocols.com/Pdf/doi/10.1007/978-1-59745-251-9_3?encCode=RklCOjNfOS0xNTItNTQ3OTUtMS04Nzk= Watch: | http://mafft.cbrc.jp/alignment/software/source.html mafft-(.*)-without-extensions-src.tgz debian/README.test0000644000000000000000000000176311703527240011034 0ustar mafft for Debian ---------------- The mafft program is tested when we assemble our binary packages in our build network. The following commands are run and compared to a reference output: mafft test/sample | diff test/sample.fftns2 - mafft --maxiterate 100 test/sample | diff test/sample.fftnsi - mafft --globalpair test/sample | diff test/sample.gins1 - mafft --globalpair --maxiterate 100 test/sample | diff test/sample.ginsi - mafft --localpair test/sample | diff test/sample.lins1 - mafft --localpair --maxiterate 100 test/sample | diff test/sample.linsi - The test sample and the reference output are distributed compressed in the mafft binary package in the ‘/usr/share/doc/mafft/test’ directory. You can copy this directory to a temporary place, uncompress the files and run the above commands to reproduce the tests on your local installation. -- Charles Plessy Mon, 14 Dec 2009 12:43:21 +0900 debian/control0000644000000000000000000000327212175725605010607 0ustar Source: mafft Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9) Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/mafft/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/mafft/trunk/ Homepage: http://mafft.cbrc.jp/alignment/software/ XS-Testsuite: autopkgtest Package: mafft Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Recommends: blast2, lynx, ruby Enhances: t-coffee Description: Multiple alignment program for amino acid or nucleotide sequences MAFFT is a multiple sequence alignment program which offers three accuracy-oriented methods: * L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information), * G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information), * E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences), and five speed-oriented methods: * FFT-NS-i (iterative refinement method; two cycles only), * FFT-NS-i (iterative refinement method; max. 1000 iterations), * FFT-NS-2 (fast; progressive method), * FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree), * NW-NS-PartTree-1 (recommended for ∼50,000 sequences; progressive method with the PartTree algorithm). debian/compat0000644000000000000000000000000212036456505010372 0ustar 9