Name:		samtools

Version:	0.1.8

Release:	1%{?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

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 efficient utilities on

manipulating alignments in the SAM format.

%prep

%setup -q

# fix wrong interpreter

perl -pi -e "s[/software/bin/python][%{__python}]" misc/varfilter.py

%build

make CFLAGS="%{optflags}" samtools razip %{?_smp_mflags}

cd misc/

make CFLAGS="%{optflags}" %{?_smp_mflags}

%install

rm -rf %{buildroot}

mkdir -p %{buildroot}%{_bindir}

install -p samtools razip %{buildroot}%{_bindir}

gzip samtools.1

mkdir -p %{buildroot}%{_mandir}/man1/

cp -p samtools.1.gz %{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								\

    %{buildroot}%{_bindir}

%clean

rm -rf %{buildroot}

%files

%defattr(-,root,root,-)

%doc AUTHORS ChangeLog COPYING INSTALL NEWS examples/ samtools.txt

%{_bindir}/*

%{_mandir}/man1/*

%changelog

* 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.