Name:		fastx_toolkit

Version:	0.0.14

Release:	15%{?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

* 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