Name: samtools Version: 1.15.1 Release: 3%{?dist} Summary: Tools for nucleotide sequence alignments in the SAM format License: MIT URL: http://www.htslib.org/ Source0: https://github.com/%{name}/%{name}/releases/download/%{version}/%{name}-%{version}.tar.bz2 BuildRequires: gcc BuildRequires: htslib-devel BuildRequires: htslib-tools BuildRequires: ncurses-devel BuildRequires: zlib-devel # It's used in make test. BuildRequires: perl-interpreter BuildRequires: perl(FindBin) BuildRequires: perl(Getopt::Long) BuildRequires: perl(lib) %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. %prep %setup -q # Remove INSTALL file to suppress rpmlint warning. rm -f INSTALL %build %configure CFLAGS="%{optflags}" LDFLAGS="%{build_ldflags}" \ --prefix=%{_prefix} \ --with-htslib=system %make_build %install %make_install # Remove misc/varfilter.py script using Python 2, # as it has not been usable since 2011. # https://github.com/samtools/samtools/commit/2c1daf5 rm -f %{buildroot}%{_bindir}/varfilter.py # Replace shebang for /usr/lib/rpm/redhat/brp-mangle-shebangs check. for file in $(grep -l '^#!/usr/bin/env perl' %{buildroot}%{_bindir}/*); do sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' "${file}" done %check # Check if samtools is built with system htslib. ldd samtools | grep -E '/lib(64)?/libhts\.so\.' make test %files %doc AUTHORS ChangeLog.old NEWS examples/ %license LICENSE # We do not use a wildcard to list bin files, because this often leads # to problems when the name changes or something additional is installed. %{_bindir}/ace2sam %{_bindir}/blast2sam.pl %{_bindir}/bowtie2sam.pl %{_bindir}/export2sam.pl %{_bindir}/fasta-sanitize.pl %{_bindir}/interpolate_sam.pl %{_bindir}/maq2sam-long %{_bindir}/maq2sam-short %{_bindir}/md5fa %{_bindir}/md5sum-lite %{_bindir}/novo2sam.pl %{_bindir}/plot-ampliconstats %{_bindir}/plot-bamstats %{_bindir}/psl2sam.pl %{_bindir}/sam2vcf.pl %{_bindir}/samtools %{_bindir}/samtools.pl %{_bindir}/seq_cache_populate.pl %{_bindir}/soap2sam.pl %{_bindir}/wgsim %{_bindir}/wgsim_eval.pl %{_bindir}/zoom2sam.pl %{_mandir}/man1/samtools.1* %{_mandir}/man1/samtools-addreplacerg.1* %{_mandir}/man1/samtools-ampliconclip.1* %{_mandir}/man1/samtools-ampliconstats.1* %{_mandir}/man1/samtools-bedcov.1* %{_mandir}/man1/samtools-calmd.1* %{_mandir}/man1/samtools-cat.1* %{_mandir}/man1/samtools-collate.1* %{_mandir}/man1/samtools-consensus.1* %{_mandir}/man1/samtools-coverage.1* %{_mandir}/man1/samtools-depad.1* %{_mandir}/man1/samtools-depth.1* %{_mandir}/man1/samtools-dict.1* %{_mandir}/man1/samtools-faidx.1* %{_mandir}/man1/samtools-fasta.1* %{_mandir}/man1/samtools-fastq.1* %{_mandir}/man1/samtools-fixmate.1* %{_mandir}/man1/samtools-flags.1* %{_mandir}/man1/samtools-flagstat.1* %{_mandir}/man1/samtools-fqidx.1* %{_mandir}/man1/samtools-head.1* %{_mandir}/man1/samtools-idxstats.1* %{_mandir}/man1/samtools-import.1* %{_mandir}/man1/samtools-index.1* %{_mandir}/man1/samtools-markdup.1* %{_mandir}/man1/samtools-merge.1* %{_mandir}/man1/samtools-mpileup.1* %{_mandir}/man1/samtools-phase.1* %{_mandir}/man1/samtools-quickcheck.1* %{_mandir}/man1/samtools-reheader.1* %{_mandir}/man1/samtools-rmdup.1* %{_mandir}/man1/samtools-samples.1* %{_mandir}/man1/samtools-sort.1* %{_mandir}/man1/samtools-split.1* %{_mandir}/man1/samtools-stats.1* %{_mandir}/man1/samtools-targetcut.1* %{_mandir}/man1/samtools-tview.1* %{_mandir}/man1/samtools-view.1* %{_mandir}/man1/wgsim.1* %changelog * Thu May 05 2022 Aram Minasyan - 1.15.1-1 - Bump the version to 1.15.1 build for EPEL/Copr, add additional bin & man files. * Tue Mar 17 2020 Jun Aruga - 1.9-3 - Fix the build failure adding perl(FindBin) and perl(lib) build dependencies. * Thu Jan 30 2020 Fedora Release Engineering - 1.9-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild * Mon Nov 04 2019 Jun Aruga - 1.9-1 - Update to 1.9 - Remove devel and libs sub packges, as "make dylib" was removed. * Fri Nov 01 2019 Jun Aruga - 0.1.19-20 - Remove Python 2 dependency (rhbz#1738176). * Fri Jul 26 2019 Fedora Release Engineering - 0.1.19-19 - Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild * Wed Jul 10 2019 Petr Pisar - 0.1.19-18 - varfilter.py is a Python 2 code (bug #1675976) * Sat Feb 02 2019 Fedora Release Engineering - 0.1.19-17 - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild * Wed Jul 25 2018 Adam Huffman - 0.1.19-16 - Add BR for python2 * Fri Jul 20 2018 Adam Huffman - 0.1.19-15 - Add BR for gcc * Sat Jul 14 2018 Fedora Release Engineering - 0.1.19-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild * Fri Feb 09 2018 Fedora Release Engineering - 0.1.19-13 - Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild * Thu Aug 03 2017 Fedora Release Engineering - 0.1.19-12 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild * Thu Jul 27 2017 Fedora Release Engineering - 0.1.19-11 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild * Sat Feb 11 2017 Fedora Release Engineering - 0.1.19-10 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild * Thu Feb 04 2016 Fedora Release Engineering - 0.1.19-9 - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild * Fri Jun 19 2015 Fedora Release Engineering - 0.1.19-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild * Fri May 29 2015 Tom Callaway - 0.1.19-7 - add fixes from Rsamtools * Mon Aug 18 2014 Fedora Release Engineering - 0.1.19-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild * Mon Jun 9 2014 Tom Callaway - 0.1.19-5 - add faidx_fetch_seq2 function from rsamtools * Sun Jun 08 2014 Fedora Release Engineering - 0.1.19-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild * Sun Aug 04 2013 Fedora Release Engineering - 0.1.19-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild * Wed Jul 17 2013 Petr Pisar - 0.1.19-2 - Perl 5.18 rebuild * Thu Apr 11 2013 Tom Callaway - 0.1.19-1 - update to 0.1.19 * Thu Feb 14 2013 Fedora Release Engineering - 0.1.18-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild * Sat Jul 21 2012 Fedora Release Engineering - 0.1.18-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild * Sat Jan 14 2012 Fedora Release Engineering - 0.1.18-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild * Wed Oct 26 2011 Adam Huffman - 0.1.18-2 - make sure new seqtk tool included * Tue Sep 6 2011 Rasmus Ory Nielsen - 0.1.18-1 - Updated to 0.1.18 * Tue May 10 2011 Rasmus Ory Nielsen - 0.1.16-1 - Updated to 0.1.16 * Mon Apr 11 2011 Rasmus Ory Nielsen - 0.1.15-1 - Updated to 0.1.15 * Wed Mar 23 2011 Rasmus Ory Nielsen - 0.1.14-1 - Updated to 0.1.14 - Build shared library instead of static * Wed Feb 09 2011 Fedora Release Engineering - 0.1.12a-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild * Mon Dec 6 2010 Rasmus Ory Nielsen - 0.1.12a-2 - Fixed header files directory ownership - Added missing header files * Mon Dec 6 2010 Rasmus Ory Nielsen - 0.1.12a-1 - Updated to 0.1.12a * Tue Nov 23 2010 Adam Huffman - 0.1.8-4 - cleanup man page handling * Sun Oct 10 2010 Adam Huffman - 0.1.8-4 - fix attributes for devel subpackage - fix library location * Sun Sep 26 2010 Adam Huffman - 0.1.8-3 - put headers and library in standard locations * Mon Sep 6 2010 Adam Huffman - 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 - 0.1.8-1 - Updated to 0.1.8. * Mon Nov 30 2009 Rasmus Ory Nielsen - 0.1.7a-1 - Updated to 0.1.7a. * Sun Jul 26 2009 Fedora Release Engineering - 0.1.5c-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild * Sun Jul 12 2009 Rasmus Ory Nielsen - 0.1.5c-3 - Specfile cleanup. * Sat Jul 11 2009 Rasmus Ory Nielsen - 0.1.5c-2 - Fixed manpage location. - Make sure optflags is passed to the makefiles. * Sat Jul 11 2009 Rasmus Ory Nielsen - 0.1.5c-1 - Initial build.