debian/0000775000000000000000000000000012315332102007160 5ustar debian/copyright0000664000000000000000000000420212273207104011117 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: snp-sites Source: https://github.com/sanger-pathogens/snp_sites Files: * Copyright: 2012-2013 Andrew Page 2013-2013 Jorge Soares License: GPL-3+ 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 3 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 program. If not, see . On Debian systems, the complete text of the GNU General Public License version 3 can be found in "/usr/share/common-licenses/GPL-3". Files: src/kseq.h Copyright: 2008-2011 Attractive Chaos License: MIT 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. debian/libsnp-sites1-dev.README.Debian0000664000000000000000000000105012273207104014473 0ustar libsnp-sites-dev for Debian --------------------------- A test folder is provided along with the snp-sites source code. You can get it from: https://github.com/sanger-pathogens/snp_sites/tree/master/tests/data The snp-sites code is still in pre-publication. The main developers of this software are: Andrew Page Jorge Soares Simon Harris Any queries just forward them to either Andrew or Jorge. -- Jorge Soares Fri, 10 Jan 2014 15:55:19 +0000 debian/snp-sites.manpages0000664000000000000000000000001412273207104012623 0ustar debian/man/*debian/snp-sites.README.Debian0000664000000000000000000000057212273207104013157 0ustar snp-sites for Debian -------------------- The snp-sites code is still in pre-publication. The main developers of this software are: Andrew Page Jorge Soares Simon Harris Any queries just forward them to either Andrew or Jorge. -- Jorge Soares Fri, 10 Jan 2014 15:55:19 +0000 debian/changelog0000664000000000000000000000076012315332005011037 0ustar snp-sites (1.5.0-1ubuntu1) trusty; urgency=low * Fix linking order for Ubuntu 14.04, resolving FTBFS. -- Daniel T Chen Fri, 28 Mar 2014 13:39:28 -0400 snp-sites (1.5.0-1) unstable; urgency=low * New upstream version Closes: #735596 -- Jorge Soares Sat, 01 Feb 2014 12:20:11 +0000 snp-sites (1.3-1) unstable; urgency=low * Initial release (Closes: #735180) -- Jorge Soares Fri, 10 Jan 2014 15:55:19 +0000 debian/docs0000664000000000000000000000001212273207104010032 0ustar README.md debian/patches/0000775000000000000000000000000012315332024010612 5ustar debian/patches/series0000664000000000000000000000002512315331574012035 0ustar linking_order.patch debian/patches/linking_order.patch0000664000000000000000000000124712315332024014465 0ustar Description: Fix linking order for Ubuntu 14.04 Author: Daniel T Chen Origin: Ubuntu Forwarded: no Last-Update: 2014-03-28 Index: snp-sites-1.5.0/src/Makefile.am =================================================================== --- snp-sites-1.5.0.orig/src/Makefile.am 2014-03-28 13:38:04.000000000 -0400 +++ snp-sites-1.5.0/src/Makefile.am 2014-03-28 13:38:04.000000000 -0400 @@ -28,4 +28,4 @@ ../tests/helper-methods.c \ ../tests/run-all-tests.c run_all_tests_CFLAGS = -I../tests -run_all_tests_LDADD = -lm -lcheck libsnp-sites.la -lz -lpthread -lrt \ No newline at end of file +run_all_tests_LDADD = -lcheck -lm libsnp-sites.la -lz -lpthread -lrt debian/watch0000664000000000000000000000017012273207104010215 0ustar version=3 https://github.com/sanger-pathogens/snp_sites/tags \ /sanger-pathogens/snp_sites/archive/([.\d]+)\.tar\.gz debian/snp-sites.install0000664000000000000000000000002112273207104012474 0ustar usr/bin/snp-sitesdebian/control0000664000000000000000000000600612315330634010575 0ustar Source: snp-sites Maintainer: Ubuntu Developers XSBC-Original-Maintainer: Debian Med Packaging Team Uploaders: Jorge Soares Section: science Priority: optional Build-Depends: debhelper (>= 9.0.0), autotools-dev, zlib1g-dev, check, dh-autoreconf, d-shlibs, libxml2-utils, docbook, docbook-xsl, xsltproc, asciidoc Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/snp-sites.git Vcs-Git: git://anonscm.debian.org/debian-med/snp-sites.git Homepage: https://github.com/sanger-pathogens/snp_sites Package: snp-sites Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, libsnp-sites1 Description: Binary code for the package snp-sites This program finds single nucleotide polymorphism (SNP) sites from multi-fasta alignment input files (which might be compressed). Its output can be in various widely used formats (Multi Fasta Alignment, Vcf, phylip). . The software has been developed at the Wellcome Trust Sanger Institute. . A Single Nucleotide - polymorphism (SNP, pronounced snip; plural snips) is a DNA sequence variation occurring when a Single Nucleotide — A, T, C or G — in the genome (or other shared sequence) differs between members of a biological species or paired chromosomes. For example, two sequenced DNA fragments from different individuals, AAGCCTA to AAGCTTA, contain a difference in a single nucleotide. In this case there are two alleles. Almost all common SNPs have only two alleles. Package: libsnp-sites1 Architecture: any Section: libs Depends: ${shlibs:Depends}, ${misc:Depends} Description: Shared libraries of the package snp-sites Snp-sites finds single nucleotide polymorphism (SNP) sites from multi-fasta alignment input files (which might be compressed). Its output can be in various widely used formats (Multi Fasta Alignment, Vcf, phylip). . The software has been developed at the Wellcome Trust Sanger Institute. . This package contains the dynamic library uses by snp-sites. Package: libsnp-sites1-dev Architecture: any Section: libdevel Depends: ${shlibs:Depends}, ${misc:Depends}, libsnp-sites1 (= ${binary:Version}) Conflicts: libsnp-sites-dev Provides: libsnp-sites-dev Description: Static libraries and header files for the package snp-sites Snp-sites finds single nucleotide polymorphism (SNP) sites from multi-fasta alignment input files (which might be compressed). Its output can be in various widely used formats (Multi Fasta Alignment, Vcf, phylip). . The software has been developed at the Wellcome Trust Sanger Institute. . This package contains the development files to include snp-sites into your own code. The library enables Python developers to make snp-sites function calls (Python bindings) through the Boost Python Library. debian/source/0000775000000000000000000000000012273207104010466 5ustar debian/source/format0000664000000000000000000000001412273207104011674 0ustar 3.0 (quilt) debian/compat0000664000000000000000000000000212273207104010364 0ustar 9 debian/rules0000775000000000000000000000104512273207104010246 0ustar #!/usr/bin/make -f # -*- makefile -*- # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 export DH_ALWAYS_EXCLUDE=.gitignore mandir := $(CURDIR)/debian/man %: dh $@ --with autoreconf override_dh_install: dh_install d-shlibmove --commit \ --multiarch \ --movedev "debian/tmp/usr/include/snp-sites/*.h" usr/include/snp-sites \ debian/tmp/usr/lib/*/libsnp-sites.so override_dh_installman: mkdir -p $(mandir) a2x --no-xmllint -f manpage $(CURDIR)/snp-sites.txt mv $(CURDIR)/snp-sites.1 $(mandir) dh_installman --