debian/0000755000000000000000000000000012171525514007171 5ustar debian/copyright0000644000000000000000000000546712171517153011140 0ustar This package was debianized by Julien Dutheil on Fri, 08 Mar 2013 11:41:00 +0100 It was downloaded from Upstream Author: Julien Dutheil Copyright: Copyright (C) 2013 Bio++ Development Team License: This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA The Debian packaging is (C) 2013, Julien Dutheil and is licensed under the GPL, see `/usr/share/common-licenses/GPL'. The provided software is distributed under the CeCILL license: This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. The complete text of the license may be found here: http://www.cecill.info/licences/Licence_CeCILL_V2-en.html debian/changelog0000644000000000000000000000345012171525514011045 0ustar bppsuite (0.8.0-1+build1) unstable; urgency=low * New models for proteins (COaLA) * New program bppMixedLikelihoods -- Julien Dutheil Fri, 08 Mar 2013 11:41:00 +0100 bppsuite (0.7.0-1) unstable; urgency=low * Several program improvements (more models, options, etc.) * New program bpp Alignment scores. -- Julien Dutheil Wed, 15 Feb 2012 09:17:00 +0100 bppsuite (0.6.2-1) unstable; urgency=low * RFP: Bio++ -- The Bio++ bioinformatics libraries. (Closes: #616373). * Packages are now non-native. -- Julien Dutheil Thu, 09 Jun 2011 11:00:00 +0100 bppsuite (0.6.1) unstable; urgency=low * Compatibility update with bpp-phyl 2.0.1. -- Julien Dutheil Mon, 28 Feb 2011 09:00:00 +0100 bppsuite (0.6.0) unstable; urgency=low * Compatibility update with Bio++ 2.0.0. * New mixed substitution models. * More sequence manipulation tools. * Several bug fixed and syntax improvements. -- Julien Dutheil Mon, 07 Feb 2011 09:00:00 +0100 bppsuite (0.5.0) unstable; urgency=low * New substitution models. * New tree drawing program. * Compatibility update with Bio++ 1.9.0. -- Julien Dutheil Thu, 25 Mar 2010 21:17:37 +0100 bppsuite (0.4.0) unstable; urgency=low * Major syntax update, using keyvals. * Compatibility update with Bio++ 1.8.0. -- Julien Dutheil Wed, 10 Jun 2009 11:28:58 +0100 bppsuite (0.3.1) unstable; urgency=low * Several bug fixed. -- Julien Dutheil Thu, 11 Dec 2008 12:21:37 +0100 bppsuite (0.3.0) unstable; urgency=low * Initial release -- Julien Dutheil Fri, 25 Sep 2008 14:28:21 +0200 debian/rules0000755000000000000000000000731012171517153010252 0ustar #!/usr/bin/make -f # -*- makefile -*- # Sample debian/rules that uses debhelper. # # This file was originally written by Joey Hess and Craig Small. # As a special exception, when this file is copied by dh-make into a # dh-make output file, you may use that output file without restriction. # This special exception was added by Craig Small in version 0.37 of dh-make. # # Modified to make a template file for a multi-binary package with separated # build-arch and build-indep targets by Bill Allombert 2001 # 25/03/10 Modification for use with CMake by Julien Dutheil. # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 # This has to be exported to make some magic below work. export DH_OPTIONS # These are used for cross-compiling and for saving the configure script # from having to guess our platform (since we know it already) DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE) DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE) CFLAGS = -Wall -g ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) CFLAGS += -O0 else CFLAGS += -O2 endif configure: cmake -DCMAKE_INSTALL_PREFIX=/usr . config.status: configure dh_testdir #Architecture build: build-arch build-indep build-arch: build-arch-stamp build-arch-stamp: config.status # Add here commands to compile the arch part of the package. #$(MAKE) touch $@ build-indep: build-indep-stamp build-indep-stamp: config.status # Add here commands to compile the indep part of the package. #$(MAKE) doc touch $@ clean: dh_testdir dh_testroot rm -f build-arch-stamp build-indep-stamp #CONFIGURE-STAMP# rm -f CMakeCache.txt # Add here commands to clean up after the build process. [ ! -f Makefile ] || $(MAKE) clean; [ ! -f Makefile ] || rm Makefile; [ ! -f bppSuite/Makefile ] || rm bppSuite/Makefile; [ ! -f doc/Makefile ] || rm doc/Makefile; [ ! -f man/Makefile ] || rm man/Makefile; rm -f man/*.gz; rm -f config.sub config.guess rm -f build-stamp rm -f CMakeCache.txt rm -f *.cmake rm -f bppSuite/*.cmake #rm -f test/*.cmake rm -f man/*.cmake rm -f doc/*.cmake rm -rf CMakeFiles rm -rf bppSuite/CMakeFiles #rm -rf test/CMakeFiles rm -rf man/CMakeFiles rm -rf doc/CMakeFiles rm -rf doc/bppsuite.info rm -rf _CPack_Packages #rm -rf Testing #rm -f DartConfiguration.tcl dh_clean install: install-indep install-arch install-indep: dh_testdir dh_testroot dh_prep -i dh_installdirs -i # Add here commands to install the indep part of the package into # debian/-doc. #INSTALLDOC# dh_install -i install-arch: dh_testdir dh_testroot dh_prep -s dh_installdirs -s # Add here commands to install the arch part of the package into # debian/tmp. $(MAKE) DESTDIR=$(CURDIR)/debian/bppsuite man doc install dh_install -s # Must not depend on anything. This is to be called by # binary-arch/binary-indep # in another 'make' thread. binary-common: dh_testdir dh_testroot dh_installchangelogs ChangeLog dh_installdocs dh_installexamples # dh_installmenu # dh_installdebconf # dh_installlogrotate # dh_installemacsen # dh_installpam # dh_installmime # dh_python # dh_installinit # dh_installcron dh_installinfo dh_installman dh_link dh_strip dh_compress dh_fixperms # dh_perl # dh_makeshlibs dh_installdeb dh_shlibdeps dh_gencontrol dh_md5sums dh_builddeb # Build architecture independant packages using the common target. binary-indep: build-indep install-indep $(MAKE) -f debian/rules DH_OPTIONS=-i binary-common # Build architecture dependant packages using the common target. binary-arch: build-arch install-arch $(MAKE) -f debian/rules DH_OPTIONS=-s binary-common binary: binary-arch binary-indep .PHONY: build clean binary-indep binary-arch binary install install-indep install-arch debian/docs0000644000000000000000000000000012171517153010032 0ustar debian/compat0000644000000000000000000000000212171517153010367 0ustar 5 debian/bppsuite.manpages0000644000000000000000000000033212171517153012537 0ustar man/bppml.1.gz man/bppseqgen.1.gz man/bppancestor.1.gz man/bppdist.1.gz man/bpppars.1.gz man/bppseqman.1.gz man/bppphysamp.1.gz man/bppreroot.1.gz man/bppconsense.1.gz man/bpptreedraw.1.gz man/bppmixedlikelihoods.1.gz debian/patches/0000755000000000000000000000000012171525075010622 5ustar debian/patches/debian-changes-0.8.0-10000644000000000000000000000331212171525075014173 0ustar Description: Upstream changes introduced in version 0.8.0-1 This patch has been created by dpkg-source during the package build. Here's the last changelog entry, hopefully it gives details on why those changes were made: . bppsuite (0.8.0-1) unstable; urgency=low . * New models for proteins (COaLA) * New program bppMixedLikelihoods . The person named in the Author field signed this changelog entry. Author: Julien Dutheil --- The information above should follow the Patch Tagging Guidelines, please checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here are templates for supplementary fields that you might want to add: Origin: , Bug: Bug-Debian: http://bugs.debian.org/ Bug-Ubuntu: https://launchpad.net/bugs/ Forwarded: Reviewed-By: Last-Update: --- bppsuite-0.8.0.orig/doc/bppsuite.texi +++ bppsuite-0.8.0/doc/bppsuite.texi @@ -1,7 +1,7 @@ \input texinfo @c -*-texinfo-*- @c %**start of header @setfilename bppsuite.info -@settitle BppSuite Manual 0.7.0 +@settitle BppSuite Manual 0.8.0 @documentencoding UTF-8 @afourpaper @dircategory Science Biology Genetics @@ -21,9 +21,9 @@ @c %**end of header @copying -This is the manual of the Bio++ Program Suite, version 0.7.0. +This is the manual of the Bio++ Program Suite, version 0.8.0. -Copyright @copyright{} 2007, 2008, 2009, 2010, 2011, 2012 Bio++ development team +Copyright @copyright{} 2007, 2008, 2009, 2010, 2011, 2012, 2013 Bio++ development team @end copying @titlepage debian/patches/series0000644000000000000000000000002712171525075012036 0ustar debian-changes-0.8.0-1 debian/control0000644000000000000000000000207312171517153010576 0ustar Source: bppsuite Section: science Priority: optional Maintainer: Loic Dachary Uploaders: Julien Dutheil Build-Depends: debhelper (>= 5), cmake (>= 2.6), dpkg (>= 1.15.4) | install-info, texinfo, libbpp-phyl-dev (>= 2.0.3) Standards-Version: 3.9.1 Package: bppsuite Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, libbpp-phyl9 (>= 2.0.3) Description: Bio++ program suite Includes programs: - BppML for maximum likelihood analysis, - BppSeqGen for sequences simulation, - BppAncestor for ancestral states reconstruction, - BppDist for distance methods, - BppPars for parsimony analysis, - BppSeqMan for file conversion and sequence manipulation, - BppConsense for building consensus tree and computing bootstrap values, - BppPhySamp for phylogenetic sampling, - BppReRoot for tree rerooting. - BppTreeDraw for tree drawing. - BppAlnScore for comparing alignments and computing alignment scores. - BppMixedLikelihoods for computing site per site likelihoods of components of mixture models. debian/source/0000755000000000000000000000000012171517154010472 5ustar debian/source/format0000644000000000000000000000001412171517153011677 0ustar 3.0 (quilt)