Name: samtools
Version: 1.9
Release: 5%{?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: make
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}/interpolate_sam.pl
%{_bindir}/maq2sam-long
%{_bindir}/maq2sam-short
%{_bindir}/md5fa
%{_bindir}/md5sum-lite
%{_bindir}/novo2sam.pl
%{_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/wgsim.1*
%changelog
* Wed Jan 27 2021 Fedora Release Engineering <releng@fedoraproject.org> - 1.9-5
- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
* Wed Jul 29 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.9-4
- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
* Tue Mar 17 2020 Jun Aruga <jaruga@redhat.com> - 1.9-3
- Fix the build failure adding perl(FindBin) and perl(lib) build dependencies.
* Thu Jan 30 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.9-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
* Mon Nov 04 2019 Jun Aruga <jaruga@redhat.com> - 1.9-1
- Update to 1.9
- Remove devel and libs sub packges, as "make dylib" was removed.
* Fri Nov 01 2019 Jun Aruga <jaruga@redhat.com> - 0.1.19-20
- Remove Python 2 dependency (rhbz#1738176).
* Fri Jul 26 2019 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.19-19
- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild
* Wed Jul 10 2019 Petr Pisar <ppisar@redhat.com> - 0.1.19-18
- varfilter.py is a Python 2 code (bug #1675976)
* Sat Feb 02 2019 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.19-17
- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild
* Wed Jul 25 2018 Adam Huffman <bloch@verdurin.com> - 0.1.19-16
- Add BR for python2
* Fri Jul 20 2018 Adam Huffman <bloch@verdurin.com> - 0.1.19-15
- Add BR for gcc
* Sat Jul 14 2018 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.19-14
- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild
* Fri Feb 09 2018 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.19-13
- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
* Thu Aug 03 2017 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.19-12
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild
* Thu Jul 27 2017 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.19-11
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild
* Sat Feb 11 2017 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.19-10
- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild
* Thu Feb 04 2016 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.19-9
- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild
* Fri Jun 19 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.1.19-8
- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild
* Fri May 29 2015 Tom Callaway <spot@fedoraproject.org> - 0.1.19-7
- add fixes from Rsamtools
* Mon Aug 18 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.1.19-6
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild
* Mon Jun 9 2014 Tom Callaway <spot@fedoraproject.org> - 0.1.19-5
- add faidx_fetch_seq2 function from rsamtools
* Sun Jun 08 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.1.19-4
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild
* Sun Aug 04 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.1.19-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild
* Wed Jul 17 2013 Petr Pisar <ppisar@redhat.com> - 0.1.19-2
- Perl 5.18 rebuild
* Thu Apr 11 2013 Tom Callaway <spot@fedoraproject.org> - 0.1.19-1
- update to 0.1.19
* Thu Feb 14 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.1.18-5
- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
* Sat Jul 21 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.1.18-4
- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild
* Sat Jan 14 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.1.18-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild
* 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.