debian/0000775000000000000000000000000012253503071007166 5ustar debian/rules0000775000000000000000000000107012064103245010243 0ustar #!/usr/bin/make -f # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 #DPKG_EXPORT_BUILDFLAGS = 1 #include /usr/share/dpkg/buildflags.mk %: dh $@ --buildsystem=cmake --parallel override_dh_auto_configure: dh_auto_configure -- \ -Dofficial_binary_packaging=on \ -Dprime_dynamic=on \ -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_INSTALL_RPATH=/usr/lib/prime-phylo \ -DCMAKE_BUILD_TYPE=RELEASE #override_dh_shlibdeps: # dh_shlibdeps -l/usr/lib/prime-phylo override_dh_makeshlibs: dh_makeshlibs -pprime-phylo -Xprime-phylo.so -Xprime-phylo-sfile.so debian/watch0000664000000000000000000000010612064103245010213 0ustar version=3 http://prime.sbc.su.se/download/prime-phylo-(.*)\.tar\.gz debian/changelog0000664000000000000000000000101512253503070011034 0ustar prime-phylo (1.0.11-1build2) trusty; urgency=medium * No-change rebuild for libopenmpi1.3 -> libopenmpi1.6 transition. -- Logan Rosen Sun, 15 Dec 2013 23:48:45 -0500 prime-phylo (1.0.11-1build1) trusty; urgency=low * No change rebuild for Boost 1.54 transition. -- Dmitrijs Ledkovs Mon, 21 Oct 2013 12:37:07 +0100 prime-phylo (1.0.11-1) unstable; urgency=low * Initial release (Closes: #684039) -- Erik Sjolund Mon, 17 Dec 2012 14:11:13 +0100 debian/upstream0000664000000000000000000000105212064103245010746 0ustar Contact: Lars Arvestad Homepage: http://prime.sbc.su.se/ Reference: Author: Åkerborg, Ö. and Sennblad, B. and Arvestad, L. and Lagergren, J. Title: "Simultaneous Bayesian gene tree reconstruction and reconciliation analysis" Journal: Proceedings of the National Academy of Sciences Year: 2009 Volume: 106 Number: 14 Pages: 5714-5719 DOI: 10.1073/pnas.0806251106 PMID: 19299507 URL: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667006/ eprint: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667006/pdf/zpq5714.pdf debian/prime-phylo.lintian-overrides0000664000000000000000000000221712064103245015014 0ustar # Adding the function fix_for_lintian_false_positive_hardening_no_fortify_functions # to src/cxx/applications/primeDLRS/primeDLRS.cc # makes the hardening-no-fortify-functions go away. It was suggested # to me that it is better remove this function and instead add a lintian override. # #/************************************************************************ # * Main program. See help message method for program description. # ************************************************************************/ # #/** The function fix_for_lintian_false_positive_hardening_no_fortify_functions # should never be called. By adding it here the program lintian will not # detect the false positive hardening-no-fortify-functions. # Read more here http://lists.debian.org/debian-devel/2012/06/msg00658.html #**/ #void fix_for_lintian_false_positive_hardening_no_fortify_functions(char *str) { # char buf[20]; # strcpy(buf, str); # fprintf(stdout, "%s\n",buf); #} prime-phylo: hardening-no-fortify-functions usr/bin/primeDLRS # We have the same issue for src/cxx/applications/primeDTLSR/idolatrous.cc prime-phylo: hardening-no-fortify-functions usr/bin/primeDTLSRdebian/compat0000664000000000000000000000000212064103245010363 0ustar 9 debian/copyright0000664000000000000000000001623412064103245011126 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: prime-phylo Upstream-Contact: Erik Sjolund Source: http://prime.sbc.su.se/download/ Files: * Copyright: 2002-2012 Lars Arvestad, Bengt Sennblad, Jens Lagergren, Peter Andersson, Mattias Franberg Erik Sjolund Joel Sjostrand, Ann-Charlotte Sonnhammer, Ikram Ullah, Orjan Akerborg License: GPL-3 Files: debian/* Copyright: 2012 Erik Sjolund License: Expat Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: . The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. . THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. Files: src/cxx/libraries/prime/PRNG.hh Copyright: 1997 - 2002 Takuji Nishimura, Makoto Matsumoto 2003 - 2012 Lars Arvestad, Bengt Sennblad, Mattias Franberg License: BSD-3-clause Files: src/cxx/libraries/prime/beep2blas.hh Copyright: 2001-2005 The Trustees of Indiana University. All rights reserved. 1998-2001 University of Notre Dame. All rights reserved Andrew Lumsdaine, Jeremy G. Siek, Lie-Quan Lee 2007-2012 Bengt Sennblad License: MTL License: GPL-3 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; version 3 dated June, 2007. . On Debian systems, the complete text of version 3 of the GNU General Public License can be found in `/usr/share/common-licenses/GPL-3'. License: BSD-3-clause Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. . 2. 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. . 3. The names of its contributors may not be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "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 COPYRIGHT OWNER OR CONTRIBUTORS 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. License: MTL Indiana University has the exclusive rights to license this product under the following license. . Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. All redistributions of source code must retain the above copyright notice, the list of authors in the original source code, this list of conditions and the disclaimer listed in this license; 2. All redistributions in binary form must reproduce the above copyright notice, this list of conditions and the disclaimer listed in this license in the documentation and/or other materials provided with the distribution; 3. Any documentation included with all redistributions must include the following acknowledgement: "This product includes software developed at the University of Notre Dame and the Pervasive Technology Labs at Indiana University. For technical information contact Andrew Lumsdaine at the Pervasive Technology Labs at Indiana University. For administrative and license questions contact the Advanced Research and Technology Institute at 1100 Waterway Blvd. Indianapolis, Indiana 46202, phone 317-274-5905, fax 317-274-5902." Alternatively, this acknowledgement may appear in the software itself, and wherever such third-party acknowledgments normally appear. 4. The name "MTL" shall not be used to endorse or promote products derived from this software without prior written permission from Indiana University. For written permission, please contact Indiana University Advanced Research & Technology Institute. 5. Products derived from this software may not be called "MTL", nor may "MTL" appear in their name, without prior written permission of Indiana University Advanced Research & Technology Institute. . Indiana University provides no reassurances that the source code provided does not infringe the patent or any other intellectual property rights of any other entity. Indiana University disclaims any liability to any recipient for claims brought by any other entity based on infringement of intellectual property rights or otherwise. . LICENSEE UNDERSTANDS THAT SOFTWARE IS PROVIDED "AS IS" FOR WHICH NO WARRANTIES AS TO CAPABILITIES OR ACCURACY ARE MADE. INDIANA UNIVERSITY GIVES NO WARRANTIES AND MAKES NO REPRESENTATION THAT SOFTWARE IS FREE OF INFRINGEMENT OF THIRD PARTY PATENT, COPYRIGHT, OR OTHER PROPRIETARY RIGHTS. INDIANA UNIVERSITY MAKES NO WARRANTIES THAT SOFTWARE IS FREE FROM "BUGS", "VIRUSES", "TROJAN HORSES", "TRAP DOORS", "WORMS", OR OTHER HARMFUL CODE. LICENSEE ASSUMES THE ENTIRE RISK AS TO THE PERFORMANCE OF SOFTWARE AND/OR ASSOCIATED MATERIALS, AND TO THE PERFORMANCE AND VALIDITY OF INFORMATION GENERATED USING SOFTWARE. debian/source/0000775000000000000000000000000012064103245010465 5ustar debian/source/format0000664000000000000000000000001312064103245011672 0ustar 3.0 (quilt)debian/links0000664000000000000000000000015012064103245010224 0ustar usr/bin/primeDLRS usr/bin/primeGSRf usr/share/man/man1/primeDLRS.1.gz usr/share/man/man1/primeGSRf.1.gz debian/control0000664000000000000000000000232312231210743010566 0ustar Source: prime-phylo Section: science Priority: optional Maintainer: Ubuntu Developers XSBC-Original-Maintainer: Debian Med Packaging Team Uploaders: Erik Sjolund Build-Depends: debhelper (>= 9.0.0), gengetopt, cmake, libblas-dev, liblapack-dev, gfortran, bison, flex, libopenmpi-dev, libxml2-dev, libboost-dev, libboost-mpi-dev, libboost-serialization-dev, zlib1g-dev Standards-Version: 3.9.3 Homepage: http://prime.sbc.su.se Package: prime-phylo Architecture: any Depends: perl, ${shlibs:Depends}, ${misc:Depends} Suggests: njplot, treeviewx, muscle, probalign, mafft, python-biopython, mrbayes, phyml, raxml Description: bayesian estimation of gene trees taking the species tree into account PrIME (Probabilistic Integrated Models of Evolution) is a package supporting inference of evolutionary parameters in a Bayesian framework using Markov chain Monte Carlo simulation. A distinguishing feature of PrIME is that the species tree is taken into account when analyzing gene trees. . The input data to PrIME is a multiple sequence alignment in FASTA format and the output data contains trees in Newick format. .