Name: fastx_toolkit Version: 0.0.14 Release: 30%{?dist} Summary: Tools to process short-reads FASTA/FASTQ files License: AGPLv3+ URL: http://hannonlab.cshl.edu/%{name}/index.html Source0: http://hannonlab.cshl.edu/%{name}/%{name}-%{version}.tar.bz2 Patch0: %{name}-gcc47.patch BuildRequires: gcc-c++ BuildRequires: libgtextutils-devel BuildRequires: perl-generators BuildRequires: make # 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 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}" %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 %files %doc AUTHORS COPYING NEWS README THANKS %{_bindir}/fast* %files galaxy %{_datadir}/%{name} %changelog * Thu Jul 21 2022 Fedora Release Engineering - 0.0.14-30 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild * Thu Jan 20 2022 Fedora Release Engineering - 0.0.14-29 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild * Wed Jul 21 2021 Fedora Release Engineering - 0.0.14-28 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild * Tue Jan 26 2021 Fedora Release Engineering - 0.0.14-27 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild * Wed Aug 26 2020 Jeff Law - 0.0.14-26 - No longer force C++11 mode * Mon Jul 27 2020 Fedora Release Engineering - 0.0.14-25 - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild * Tue Jan 28 2020 Fedora Release Engineering - 0.0.14-24 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild * Thu Jul 25 2019 Fedora Release Engineering - 0.0.14-23 - Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild * Thu Jan 31 2019 Fedora Release Engineering - 0.0.14-22 - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild * Sat Jul 21 2018 Adam Huffman - 0.0.14-21 - Add BR for gcc-c++ * Fri Jul 13 2018 Fedora Release Engineering - 0.0.14-20 - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild * Wed Feb 07 2018 Fedora Release Engineering - 0.0.14-19 - Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild * Wed Aug 02 2017 Fedora Release Engineering - 0.0.14-18 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild * Wed Jul 26 2017 Fedora Release Engineering - 0.0.14-17 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild * Fri Feb 10 2017 Fedora Release Engineering - 0.0.14-16 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild * Wed Feb 03 2016 Fedora Release Engineering - 0.0.14-15 - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild * Wed Jun 17 2015 Fedora Release Engineering - 0.0.14-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild * Sat May 02 2015 Kalev Lember - 0.0.14-13 - Rebuilt for GCC 5 C++11 ABI change * Sat Aug 16 2014 Fedora Release Engineering - 0.0.14-12 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild * Sat Jun 07 2014 Fedora Release Engineering - 0.0.14-11 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild * Mon Jun 02 2014 Adam Huffman - 0.0.14-1 - Update to upstream 0.0.14 release - C++11 standard required * Sat Aug 03 2013 Fedora Release Engineering - 0.0.13-10 - Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild * Wed Jul 17 2013 Petr Pisar - 0.0.13-9 - Perl 5.18 rebuild * Wed Feb 13 2013 Fedora Release Engineering - 0.0.13-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild * Thu Jul 19 2012 Fedora Release Engineering - 0.0.13-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild * Tue Feb 28 2012 Fedora Release Engineering - 0.0.13-6 - Rebuilt for c++ ABI breakage * Mon Jan 9 2012 Adam Huffman - 0.0.13-5 - fix compilation with GCC 4.7 * Fri May 27 2011 Adam Huffman - 0.0.13-4 - fix ownership of /usr/share/fastx_toolkit * Tue Nov 16 2010 Adam Huffman - 0.0.13-3 - fix license and remove autotools Makefiles * Wed Aug 25 2010 Adam Huffman - 0.0.13-2 - fix CFLAGS and CXXFLAGS * Tue May 11 2010 Adam Huffman - 0.0.13-1 - initial version