debian/0000755000000000000000000000000012252706154007172 5ustar debian/copyright0000644000000000000000000000252311744725256011140 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://claire.bardel.free.fr/files/ Files: * Copyright: © 2005-2008 Claire Bardel © 2005-2007 Vincent Danjean License: GPL-2+ 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. Comment: On Debian systems, the complete text of the GNU General Public License version 2 can be found in ‘/usr/share/common-licenses/GPL-2’. Files: debian/* Copyright: © 2005—2008 Vincean Danjean © 2008 David Paleino © 2008–2009 Charles Plessy License: Same Same as altree itself debian/altree.bash-completion0000644000000000000000000000002711211457717013455 0ustar bash_completion altree debian/altree.docs0000644000000000000000000000004011746002721011306 0ustar README Documentation/manual.pdf debian/changelog0000644000000000000000000001347312252706135011053 0ustar altree (1.3.1-1) unstable; urgency=low * New upstream release + fix a SEGV when ALTREE_PARALLEL is used with more processors than requested permutations (-r program parameter) + Fix "FTBFS with perl 5.12.0-1: long doubles" (Closes: #578550) * debian/control: Add B-D on libtest-deep-perl (required when fixing 578550) -- Vincent Danjean Fri, 13 Dec 2013 23:27:04 +0100 altree (1.3.0-1) unstable; urgency=low * New upstream release + Mostly performance improvment * debian/control: + bump Standard-Version (no change needed) + put canonical vcs fields + remove outdated DM-Upload-Allowed field + improve altree-examples long description + add libgsl0-dev and libatlas-base-dev as new build-dependency + remove libpdl-stats-perl as (build-)dependency -- Vincent Danjean Fri, 22 Nov 2013 23:57:43 +0100 altree (1.2.1-1) unstable; urgency=low [ Andreas Tille ] * debian/upstream: Add eprint * debian/reference: Removed in favour of debian/upstream [ Vincent Danjean ] * New (stable) upstream release 1.2.1 * debian/{README.Debian,watch}: No need to skip old last version 1.1.1 * debian/patches/*: latex bug fixed upstream -- Vincent Danjean Sat, 09 Jun 2012 22:45:06 +0200 altree (1.0.1-7) unstable; urgency=low [ Thorsten Alteholz ] * debian/rules: target get-orig-source added [ Charles Plessy ] * Renamed debian/upstream-metadata.yaml to debian/upstream [ Andreas Tille ] * debian/upstream: Single Reference field instead of Reference-* * debian/watch: Do not download version 1.1.1 as the author has asked for in http://lists.debian.org/debian-med/2009/08/msg00104.html * debian/README.Debian: Document the "do not package new version" issue * debian/control: Standards-Version: 3.9.3 (no changes needed) * debian/changelog: Verified DEP5 using cme fix dpkg-copyright * debian/patches/build-with-recent-tetex.patch: Drop dvips option Closes: #669551 * debhelper 9 (control+compat) -- Andreas Tille Sun, 22 Apr 2012 08:40:48 +0200 altree (1.0.1-5) unstable; urgency=low * Upload source package without 3.0 (quilt) autopatch leftover. Closes: #643045. * Corrected VCS URLs in debian/control. * Use Debhelper 8 (debian/control, debian/compat). * Converted debian/copyright to machine-readable format 1.0 (DEP 5). * Compress binary packages with xz (debian/rules). * Conforms with Policy 3.9.2 (debian/control, no other changes needed). -- Charles Plessy Tue, 27 Sep 2011 08:31:14 +0900 altree (1.0.1-4) unstable; urgency=low [ Charles Plessy ] * Depends on libtamuanova-perl (debian/control). * Added a BibTeX reference in debian/reference and install it through debian/altree.docs. * Refreshed debian/copyright. * Using debhelper 7 (debian/compat, debian/control). * Incremented Standards-Version to reflect conformance to Policy 3.8.1 (no changes needed). * Bash completion: - Build-depend on bash-completion >= 1:1 in debian/control. - Install the altree completion file using dh_bash-completion. * Added information about Upstream in debian/upstream-metadata.yaml. [ David Paleino ] * debian/control: - removed unneeded Build-Dependencies - added ${misc:Depends} dependency to altree-examples - removed myself from Uploaders * debian/rules: - removing unneeded included Makefile [Andreas Tille] * use short debhelper instead of cdbs because the install target did not worked properly any more * debian/source/format: 3.0 (quilt) * debian/control: - Standards-Version: 3.9.1 - Added myself to Uploaders - Added Build-Depends: ghostscript to avoid errors in LaTeX run Closes: #614538 - Removed libtamuanova-perl from Depends again because it has no installation candidate -- Andreas Tille Tue, 22 Feb 2011 14:37:21 +0100 altree (1.0.1-3) unstable; urgency=low [ Charles Plessy ] * Initial release for Debian (Closes: #461506) * debian/copyright: converted to machine-readable format. * debian/control: - Added texlive-lang-french, texlive-latex-base, texlive-latex-recommended and texlive-latex-extra as build dependencies. - Updated my email address. [ David Paleino ] * Added debian/watch * debian/compat and debhelper dependency updated * debian/control: - added myself in Uploaders - Standards-Version is now 3.7.3 [ Vincent Danjean ] * remove unused debian/control.in file * Fix copyright (and update email addresses) * Fix build-depends: + remove debian part of version (thanks lintian) + change latex-utils to latex-make (always present with this name in Debian) * Fix depends: add ${perl:Depends} * remove empty dir in package (/usr/sbin) => package lintian clean now -- Vincent Danjean Mon, 12 May 2008 08:19:31 +0200 altree (1.0.1-1) unstable; urgency=low * New upstream release -- Vincent Danjean Fri, 13 Jan 2006 15:46:52 +0100 altree (1.0.0-1) unstable; urgency=low * New upstream release -- Vincent Danjean Fri, 13 Jan 2006 09:40:02 +0100 altree (0.9.2-2) unstable; urgency=low * Update FSF address in copyright file -- Vincent Danjean Sat, 10 Sep 2005 10:25:23 +0200 altree (0.9.2-1) unstable; urgency=low * New upstream release * New upstream name -- Vincent Danjean Tue, 2 Aug 2005 19:52:19 +0200 alphy (0.9.1d-1) unstable; urgency=low * New upstream release -- Vincent Danjean Tue, 26 Jul 2005 00:08:40 +0200 alphy (0.9.1c-1) unstable; urgency=low * Initial release -- Vincent Danjean Mon, 25 Jul 2005 22:22:50 +0200 debian/rules0000755000000000000000000000102111717241661010246 0ustar #!/usr/bin/make -f # -*- makefile -*- # debian/rules file for altree # Andreas Tille # GPL %: dh $@ override_dh_auto_clean: $(MAKE) -C Documentation distclean dh_auto_clean override_dh_auto_build: $(MAKE) -C Documentation pdf dh_auto_build override_dh_auto_install: $(MAKE) PREFIX=debian/altree/usr install override_dh_compress: dh_compress --exclude=.pdf override_dh_builddeb: dh_builddeb -- -Z xz get-orig-source: mkdir -p ../tarballs uscan --verbose --force-download --destdir=../tarballs debian/upstream0000644000000000000000000000124411746001676010762 0ustar Contact: Claire Bardel Homepage: http://claire.bardel.free.fr/software.html Name: ALTree Reference: DOI: 10.1093/bioinformatics/btl131 PMID: 16595555 Author: Bardel, Claire and Danjean, Vincent and Genin, Emmanuelle Journal: Bioinformatics Number: 11 Pages: 1402-1403 Title: > ALTree: association detection and localization of susceptibility sites using haplotype phylogenetic trees URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/11/1402 eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/22/11/1402.pdf Volume: 22 Year: 2006 Watch: http://claire.bardel.free.fr/files/altree-([[:digit:]].*)\.tar\.gz debian/control0000644000000000000000000000356712252706135010607 0ustar Source: altree Section: science Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Vincent Danjean , Andreas Tille Build-Depends: bash-completion, debhelper (>= 9), latex-make, ghostscript, texlive-lang-french, texlive-latex-extra, texlive-latex-recommended, texlive-fonts-recommended, libmath-tamuanova-perl, libgsl0-dev, libatlas-base-dev, libtest-deep-perl Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/altree/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/altree/trunk/ Homepage: http://claire.bardel.free.fr/software.html Package: altree Architecture: any Conflicts: libcutils-perl, alphy Replaces: libcutils-perl, alphy Provides: libcutils-perl, alphy Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}, libmath-tamuanova-perl Suggests: altree-examples Description: program to perform phylogeny-based association and localization analysis ALTree was designed to perform association detection and localization of susceptibility sites using haplotype phylogenetic trees: first, it allows the detection of an association between a candidate gene and a disease, and second, it enables to make hypothesis about the susceptibility loci. Package: altree-examples Architecture: all Recommends: altree (= ${binary:Version}) Depends: ${misc:Depends} Description: example files for ALTree ALTree was designed to perform association detection and localization of susceptibility sites using haplotype phylogenetic trees: first, it allows the detection of an association between a candidate gene and a disease, and second, it enables to make hypothesis about the susceptibility loci. . This package contains the example files for the ALTree package discussed in its PDF manual. debian/watch0000644000000000000000000000011112243747465010226 0ustar version=3 http://claire.bardel.free.fr/files/altree-v?([\d.]+)\.tar\.gz debian/source/0000755000000000000000000000000012252706152010470 5ustar debian/source/format0000644000000000000000000000001411640206671011677 0ustar 3.0 (quilt) debian/patches/0000755000000000000000000000000012252706152010617 5ustar debian/compat0000644000000000000000000000000211744730341010370 0ustar 9 debian/altree-examples.docs0000644000000000000000000000000711027133206013120 0ustar test/* debian/altree.doc-base0000644000000000000000000000100511027133206012030 0ustar Document: altree Title: ALTree: Association and Localisation tests using haplotype phylogenetic Trees Author: Claire Bardel, Vincent Danjean, Pierre Darly and Emanuelle Guérin Abstract: This manual covers the installation and usage of ALTree. It provides a reference for for the `ALTree-convert', `ALTree-add-S' and `ALTree' programs, as well as explanation about the example files distributed in the `altree-examples' Debian package. Section: Science/Biology Format: PDF Files: /usr/share/doc/altree/manual.pdf