Name: samtools Version: 0.1.18 Release: 2%{?dist} Summary: Tools for nucleotide sequence alignments in the SAM format Group: Applications/Engineering License: MIT URL: http://samtools.sourceforge.net/ Source0: http://downloads.sourceforge.net/%{name}/%{name}-%{version}.tar.bz2 Patch0: samtools-0.1.14-soname.patch BuildRoot: %(mktemp -ud %{_tmppath}/%{name}-%{version}-%{release}-XXXXXX) BuildRequires: zlib-devel >= 1.2.3 BuildRequires: ncurses-devel %description SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. %package devel Summary: Header files and libraries for compiling against %{name} Group: Development/Libraries Requires: %{name}-libs = %{version}-%{release} %description devel Header files and libraries for compiling against %{name} %package libs Summary: Libraries for applications using %{name} Group: System Environment/Libraries %description libs Libraries for applications using %name %prep %setup -q %patch0 -p1 -b .soname # fix wrong interpreter perl -pi -e "s[/software/bin/python][%{__python}]" misc/varfilter.py # fix eol encoding sed -i 's/\r//' misc/export2sam.pl %build make CFLAGS="%{optflags}" dylib %{?_smp_mflags} make CFLAGS="%{optflags} -fPIC" samtools razip %{?_smp_mflags} cd misc/ make CFLAGS="%{optflags} -fPIC" %{?_smp_mflags} cd ../bcftools make CFLAGS="%{optflags} -fPIC" %{?_smp_mflags} %install rm -rf %{buildroot} mkdir -p %{buildroot}%{_bindir} install -p samtools razip %{buildroot}%{_bindir} # header and library files mkdir -p %{buildroot}%{_includedir}/%{name} install -p -m 644 *.h %{buildroot}%{_includedir}/%{name} mkdir -p %{buildroot}%{_libdir} strip libbam.so.1 install -p -m 755 libbam.so.1 %{buildroot}%{_libdir} ln -sf libbam.so.1 %{buildroot}%{_libdir}/libbam.so mkdir -p %{buildroot}%{_mandir}/man1/ cp -p samtools.1 %{buildroot}%{_mandir}/man1/ #cp -p bcftools/bcftools.1 %{buildroot}%{_mandir}/man1/ cd misc/ install -p blast2sam.pl bowtie2sam.pl export2sam.pl interpolate_sam.pl \ maq2sam-long maq2sam-short md5fa md5sum-lite novo2sam.pl psl2sam.pl \ sam2vcf.pl samtools.pl soap2sam.pl varfilter.py wgsim wgsim_eval.pl \ zoom2sam.pl seqtk \ %{buildroot}%{_bindir} cd ../bcftools/ install -p bcftools vcfutils.pl %{buildroot}%{_bindir} mv README README.bcftools %clean rm -rf %{buildroot} %post libs -p /sbin/ldconfig %postun libs -p /sbin/ldconfig %files %defattr(-,root,root,-) %doc AUTHORS ChangeLog COPYING INSTALL NEWS examples/ bcftools/README.bcftools bcftools/bcf.tex %{_bindir}/* %{_mandir}/man1/* %files devel %defattr(-,root,root,-) %{_includedir}/%{name} %{_libdir}/libbam.so %files libs %defattr(-,root,root,-) %{_libdir}/libbam.so.* %changelog * Wed Oct 26 2011 Adam Huffman <verdurin@fedoraproject.org> - 0.1.18-2 - make sure new seqtk tool included * Tue Sep 6 2011 Rasmus Ory Nielsen <ron@ron.dk> - 0.1.18-1 - Updated to 0.1.18 * Tue May 10 2011 Rasmus Ory Nielsen <ron@ron.dk> - 0.1.16-1 - Updated to 0.1.16 * Mon Apr 11 2011 Rasmus Ory Nielsen <ron@ron.dk> - 0.1.15-1 - Updated to 0.1.15 * Wed Mar 23 2011 Rasmus Ory Nielsen <ron@ron.dk> - 0.1.14-1 - Updated to 0.1.14 - Build shared library instead of static * Wed Feb 09 2011 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.1.12a-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild * Mon Dec 6 2010 Rasmus Ory Nielsen <ron@ron.dk> - 0.1.12a-2 - Fixed header files directory ownership - Added missing header files * Mon Dec 6 2010 Rasmus Ory Nielsen <ron@ron.dk> - 0.1.12a-1 - Updated to 0.1.12a * Tue Nov 23 2010 Adam Huffman <bloch@verdurin.com> - 0.1.8-4 - cleanup man page handling * Sun Oct 10 2010 Adam Huffman <bloch@verdurin.com> - 0.1.8-4 - fix attributes for devel subpackage - fix library location * Sun Sep 26 2010 Adam Huffman <bloch@verdurin.com> - 0.1.8-3 - put headers and library in standard locations * Mon Sep 6 2010 Adam Huffman <bloch@verdurin.com> - 0.1.8-2 - merge Rasmus' latest changes (0.1.8 update) - include bam.h and libbam.a for Bio-SamTools compilation - move bam.h and libbam.a to single directory - put bgzf.h, khash.h and faidx.h in the same place - add -fPIC to CFLAGS to make Bio-SamTools happy - add virtual Provide as per guidelines * Tue Aug 17 2010 Rasmus Ory Nielsen <ron@ron.dk> - 0.1.8-1 - Updated to 0.1.8. * Mon Nov 30 2009 Rasmus Ory Nielsen <ron@ron.dk> - 0.1.7a-1 - Updated to 0.1.7a. * Sun Jul 26 2009 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.1.5c-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild * Sun Jul 12 2009 Rasmus Ory Nielsen <ron@ron.dk> - 0.1.5c-3 - Specfile cleanup. * Sat Jul 11 2009 Rasmus Ory Nielsen <ron@ron.dk> - 0.1.5c-2 - Fixed manpage location. - Make sure optflags is passed to the makefiles. * Sat Jul 11 2009 Rasmus Ory Nielsen <ron@ron.dk> - 0.1.5c-1 - Initial build.