Name: fastx_toolkit
Version: 0.0.14
Release: 16%{?dist}
Summary: Tools to process short-reads FASTA/FASTQ files
Group: Applications/Engineering
License: AGPLv3+
URL: http://hannonlab.cshl.edu/%{name}/index.html
Source0: http://hannonlab.cshl.edu/%{name}/%{name}-%{version}.tar.bz2
Patch0: %{name}-gcc47.patch
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
BuildRequires: libgtextutils-devel
BuildRequires: perl-generators
# FASTX-Barcode-Splitter requires the GNU Sed program.
Requires: sed
# fasta_clipping_histogram requires PerlIO::gzip and GD::Graph::bars
Requires: perl-PerlIO-gzip
Requires: perl-GDGraph
%description
The FASTX-Toolkit is a collection of command line tools for
Short-Reads FASTA/FASTQ files preprocessing.
Next-Generation sequencing machines usually produce FASTA or FASTQ
files, containing multiple short-reads sequences (possibly with
quality information).
The main processing of such FASTA/FASTQ files is mapping (aka
aligning) the sequences to reference genomes or other databases using
specialized programs. Example of such mapping programs are: Blat,
SHRiMP, LastZ, MAQ and many many others.
However, It is sometimes more productive to preprocess the FASTA/FASTQ
files before mapping the sequences to the genome - manipulating the
sequences to produce better mapping results.
The FASTX-Toolkit tools perform some of these preprocessing tasks.
%package galaxy
Summary: Integrate fastx_toolkit with a local Galaxy installation
Group: Applications/Engineering
Requires: %{name} = %{version}-%{release}
%description galaxy
These files allow the integration of fastx_toolkit with a local
installation of Galaxy (http://main.g2.bx.psu.edu/), a web-based
platform for analyzing multiple alignments, comparing genomic
annotations, profiling metagenomic samples and much more.
%prep
%setup -q
#Patch to fix compilation with GCC 4.7
%patch0 -p1 -b .%{name}-gcc47.patch
%build
%configure
make %{?_smp_mflags} CFLAGS="%{optflags}" CXXFLAGS="%{optflags} -std=c++11"
%install
rm -rf %{buildroot}
make install DESTDIR=%{buildroot} INSTALL="install -p"
mkdir %{buildroot}/%{_datadir}/%{name}
cp -a galaxy/ %{buildroot}/%{_datadir}/%{name}
# remove unnecessary m4 files
rm %{buildroot}/%{_datadir}/aclocal/*.m4
# remove autotools Makefile
find %{buildroot}/%{_datadir}/%{name}/galaxy/ -name "Makefile\.*" -delete
%clean
rm -rf %{buildroot}
%files
%defattr(-,root,root,-)
%doc AUTHORS COPYING NEWS README THANKS
%{_bindir}/fast*
%files galaxy
%defattr(-,root,root,-)
%{_datadir}/%{name}
%changelog
* Fri Feb 10 2017 Fedora Release Engineering <releng@fedoraproject.org> - 0.0.14-16
- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild
* Wed Feb 03 2016 Fedora Release Engineering <releng@fedoraproject.org> - 0.0.14-15
- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild
* Wed Jun 17 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.0.14-14
- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild
* Sat May 02 2015 Kalev Lember <kalevlember@gmail.com> - 0.0.14-13
- Rebuilt for GCC 5 C++11 ABI change
* Sat Aug 16 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.0.14-12
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild
* Sat Jun 07 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.0.14-11
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild
* Mon Jun 02 2014 Adam Huffman <bloch@verdurin.com> - 0.0.14-1
- Update to upstream 0.0.14 release
- C++11 standard required
* Sat Aug 03 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.0.13-10
- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild
* Wed Jul 17 2013 Petr Pisar <ppisar@redhat.com> - 0.0.13-9
- Perl 5.18 rebuild
* Wed Feb 13 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.0.13-8
- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
* Thu Jul 19 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.0.13-7
- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild
* Tue Feb 28 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.0.13-6
- Rebuilt for c++ ABI breakage
* Mon Jan 9 2012 Adam Huffman <verdurin@fedoraproject.org> - 0.0.13-5
- fix compilation with GCC 4.7
* Fri May 27 2011 Adam Huffman <bloch@verdurin.com> - 0.0.13-4
- fix ownership of /usr/share/fastx_toolkit
* Tue Nov 16 2010 Adam Huffman <bloch@verdurin.com> - 0.0.13-3
- fix license and remove autotools Makefiles
* Wed Aug 25 2010 Adam Huffman <bloch@verdurin.com> - 0.0.13-2
- fix CFLAGS and CXXFLAGS
* Tue May 11 2010 Adam Huffman <bloch@verdurin.com> - 0.0.13-1
- initial version