debian/0000755000000000000000000000000011735666401007177 5ustar debian/README.Debian0000644000000000000000000000120611556264003011230 0ustar RAxML for Debian ---------------- This version of RAxML comes without a documentation. The homepage http://wwwkramer.in.tum.de/exelixis/software.html contains several useful hints like For the most basic RAxML commands see the old v704 manual http://icwww.epfl.ch/%7Estamatak/index-Dateien/countManual7.0.4.php RAxML step-by-step tutorial http://wwwkramer.in.tum.de/exelixis/hands-On.html There are freely accessible web-servers available for RAxML at http://phylobench.vital-it.ch/raxml-bb/ and http://8ball.sdsc.edu:8889/cipres-web/Bootstrap.do . -- Andreas Tille Thu, 28 Apr 2011 14:29:21 +0200 debian/source/0000755000000000000000000000000011735664767010514 5ustar debian/source/format0000644000000000000000000000001411301174376011677 0ustar 3.0 (quilt) debian/install0000644000000000000000000000005011252160305010545 0ustar raxmlHPC usr/bin debian/dirs0000644000000000000000000000002411252162457010053 0ustar usr/share/man/man1 debian/copyright0000644000000000000000000000272111735666000011127 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: RAxML Upstream-Contact: Alexandros Stamatakis Source: http://wwwkramer.in.tum.de/exelixis/software.html Files: dmtcpaware.h Copyright: © 2009 Jason Ansel, Kapil Arya, and Gene Cooperman License: PD This file, dmtcpaware.h, is placed in the public domain. The motivation for this is to allow anybody to freely use this file without restriction to statically link this file with any software. Files: debian/* Copyright: © 2011 Andreas Tille License: GPL-2+ License: GPL-2+ This program 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 program 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 program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. . On Debian systems, the complete text of the GNU General Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'. debian/upstream0000644000000000000000000000111411735663517010764 0ustar Contact: Alexandros Stamatakis Homepage: http://wwwkramer.in.tum.de/exelixis/software.html Name: RAxML Reference: author: Alexandros Stamatakis title: > RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models journal: Bioinformatics volume: 22 number: 21 pages: 2688-2690 year: 2006 PMID: 16928733 DOI: 10.1093/bioinformatics/btl446 URL: http://bioinformatics.oxfordjournals.org/content/22/21/2688.full eprint: http://bioinformatics.oxfordjournals.org/content/22/21/2688.full.pdf+html debian/rules0000755000000000000000000000144711735666200010262 0ustar #!/usr/bin/make -f # Copyright (C) Andreas Tille # License: GPL exe=raxmlHPC %: dh $@ override_dh_auto_clean: $(MAKE) -f Makefile.gcc clean override_dh_auto_build: $(MAKE) -f Makefile.gcc override_dh_auto_install: help2man --no-info --help-option="-h" --version-option="-v" \ --name="Randomized Axelerated Maximum Likelihood" \ $(CURDIR)/$(exe) > $(CURDIR)/debian/`dh_listpackages`/usr/share/man/man1/$(exe).1 get-orig-source: mkdir -p ../tarballs uscan --verbose --force-download --destdir=../tarballs ## Upstream suggests to package what is called alpha on the web page #@echo "The watch file fails in reporting non-Alpha versions." #@echo "Just go to http://sco.h-its.org/exelixis/software.html" #@echo "and download the latest non-Alpha version." debian/watch0000644000000000000000000000056211735664226010236 0ustar version=3 opts="filenamemangle=s/countSource(.*).php/raxml-$1\.tar\.bz2/,dversionmangle=s/\.//g" \ http://sco.h-its.org/exelixis/software.html .*countSource(\d+)\.php #opts="downloadurlmangle=s/RAxML v *(\d+)\.(\d+)\.(\d+) source code now available for download/countSource$1$2$3.php/" \ # http://wwwkramer.in.tum.de/exelixis/software.html .*countSource(\d+)\.php debian/changelog0000644000000000000000000000222311735665511011051 0ustar raxml (7.2.8-2) unstable; urgency=low [ Charles Plessy ] * renamed debian/upstream-metadata.yaml to debian/upstream [ Andreas Tille ] * debian/upstream: Fixed citation information * debian/watch: Fixed upstream URL * debian/control: - Standards-Version: 3.9.3 (no changes needed) - Fixed Vcs fields * debian/rules: use uscan in get-orig-source target * debhelper 9 (control+compat) -- Andreas Tille Sat, 31 Mar 2012 22:22:07 +0200 raxml (7.2.8-1) unstable; urgency=low * New upstream version * debian/copyright: Mention dmtcpaware.h as public domain * debian/watch: tried to fix download but finally failed. Now at least the correct version number is obtained. * debian/control: Mark as buildable only on amd64 and i386 architectures (linux and bsd kernel) - SSE support is required for this package. Thanks to Marcin Juszkiewicz for the patch Closes: #626672 (LP: #791321) -- Andreas Tille Thu, 30 Jun 2011 16:10:28 +0200 raxml (7.2.6-1) unstable; urgency=low * Initial release (Closes: #624435) -- Andreas Tille Thu, 28 Apr 2011 14:29:21 +0200 debian/compat0000644000000000000000000000000211735665420010375 0ustar 9 debian/control0000644000000000000000000000147411735665461010615 0ustar Source: raxml Section: science Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Andreas Tille Build-Depends: debhelper (>= 9), help2man Standards-Version: 3.9.3 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/raxml/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/raxml/trunk/ Homepage: http://wwwkramer.in.tum.de/exelixis/software.html Package: raxml Architecture: amd64 i386 kfreebsd-i386 kfreebsd-amd64 Depends: ${shlibs:Depends}, ${misc:Depends} Description: Randomized Axelerated Maximum Likelihood of phylogenetic trees RAxML is a program for sequential and parallel Maximum Likelihood-based inference of large phylogenetic trees. It has originally been derived from fastDNAml.