Name: mmseq Version: 1.0.11 Release: 19%{?dist} Summary: Haplotype and isoform specific expression estimation for RNA-seq %if 0%{?fedora} >= 33 %bcond_without flexiblas %endif License: GPLv2+ URL: https://github.com/eturro/%{name} Source0: https://github.com/eturro/%{name}/archive/%{version}.zip #Patch1: mmseq-flags.patch Patch2: mmseq-zlib.patch BuildRequires: gcc-c++ BuildRequires: make BuildRequires: boost-devel BuildRequires: perl-generators BuildRequires: htslib-devel BuildRequires: gsl-devel BuildRequires: zlib-devel BuildRequires: armadillo-devel %if %{with flexiblas} BuildRequires: flexiblas-devel %endif Requires: ruby Requires: samtools Requires: perl-interpreter %description Software for fast, scalable haplotype and isoform expression estimation using multi-mapping RNA-seq reads. Example scripts are included. %prep %setup -q -n %{name}-%{version} #Use Fedora compilation headers #%%patch1 -p1 -b .mmseq-flags.patch #Fix zlib linking %patch -P2 -p1 -b .mmseq-zlib.patch # Remove bundled binaries # Only 2 bin/*-linux files are included in Source0 archive. rm -f bin/*-linux %if %{with flexiblas} sed -e 's/-lblas/-lflexiblas/g' -e 's/-llapack/-lflexiblas/g' -i src/Makefile %endif %build cd src make %{?_smp_mflags} CXXFLAGS="%{optflags}" %check # Check src/VERSION is correctly set. test "$(bin/mmseq --version 2>&1 || true)" = "%{name}-%{version}" %install rm -rf %{buildroot} mkdir -p %{buildroot}%{_bindir} install -p -m 0755 bin/bam2hits %{buildroot}%{_bindir} install -p -m 0755 bin/extract_transcripts %{buildroot}%{_bindir} install -p -m 0755 bin/hitstools %{buildroot}%{_bindir} install -p -m 0755 bin/mmcollapse %{buildroot}%{_bindir} install -p -m 0755 bin/mmdiff %{buildroot}%{_bindir} install -p -m 0755 bin/mmseq %{buildroot}%{_bindir} install -p -m 0755 bin/offsetGTF %{buildroot}%{_bindir} install -p -m 0755 bin/t2g_hits %{buildroot}%{_bindir} install -p -m 0755 bin/*.sh %{buildroot}%{_bindir} install -p -m 0755 bin/*.rb %{buildroot}%{_bindir} install -p -m 0755 bin/ensembl_gtf_to_gff.pl %{buildroot}%{_bindir} %files %doc README.md COPYING doc/ %{_bindir}/bam2hits %{_bindir}/extract_transcripts %{_bindir}/hitstools %{_bindir}/mmcollapse %{_bindir}/mmdiff %{_bindir}/mmseq %{_bindir}/offsetGTF %{_bindir}/t2g_hits %{_bindir}/fastagrep.sh %{_bindir}/mouse_strain_transcriptome.sh %{_bindir}/usage.sh %{_bindir}/filterGTF.rb %{_bindir}/haploref.rb %{_bindir}/testregexp.rb %{_bindir}/ensembl_gtf_to_gff.pl %changelog * Thu Jan 25 2024 Fedora Release Engineering - 1.0.11-19 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild * Sun Jan 21 2024 Fedora Release Engineering - 1.0.11-18 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild * Thu Jan 18 2024 Jonathan Wakely - 1.0.11-17 - Rebuilt for Boost 1.83 * Thu Jul 20 2023 Fedora Release Engineering - 1.0.11-16 - Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild * Mon Feb 20 2023 Jonathan Wakely - 1.0.11-15 - Rebuilt for Boost 1.81 * Thu Jan 19 2023 Fedora Release Engineering - 1.0.11-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild * Tue Aug 23 2022 Mamoru TASAKA - 1.0.11-13 - Rebuild for gsl-2.7.1 * Thu Jul 21 2022 Fedora Release Engineering - 1.0.11-12 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild * Wed May 04 2022 Thomas Rodgers - 1.0.11-11 - Rebuilt for Boost 1.78 * Thu Jan 20 2022 Fedora Release Engineering - 1.0.11-10 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild * Sat Aug 07 2021 Jonathan Wakely - 1.0.11-9 - Rebuilt for Boost 1.76 * Thu Jul 22 2021 Fedora Release Engineering - 1.0.11-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild * Tue Jan 26 2021 Fedora Release Engineering - 1.0.11-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild * Fri Jan 22 2021 Jonathan Wakely - 1.0.11-6 - Rebuilt for Boost 1.75 * Thu Aug 27 2020 Iñaki Úcar - 1.0.11-5 - https://fedoraproject.org/wiki/Changes/FlexiBLAS_as_BLAS/LAPACK_manager * Tue Jul 28 2020 Fedora Release Engineering - 1.0.11-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild * Thu May 28 2020 Jonathan Wakely - 1.0.11-3 - Rebuilt for Boost 1.73 * Wed Jan 29 2020 Fedora Release Engineering - 1.0.11-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild * Mon Nov 11 2019 Jun Aruga - 1.0.11-1 - Update to new Github-based upstream release 1.0.11. * Tue Aug 20 2019 Susi Lehtola - 1.0.8a-31 - Rebuilt for GSL 2.6. * Thu Jul 25 2019 Fedora Release Engineering - 1.0.8a-30 - Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild * Fri Feb 01 2019 Fedora Release Engineering - 1.0.8a-29 - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild * Fri Jan 25 2019 Jonathan Wakely - 1.0.8a-28 - Rebuilt for Boost 1.69 * Fri Aug 17 2018 José Abílio Matos - 1.0.8a-27 - rebuild for armadillo soname bump * Fri Jul 13 2018 Fedora Release Engineering - 1.0.8a-26 - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild * Thu Feb 08 2018 Fedora Release Engineering - 1.0.8a-25 - Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild * Tue Jan 23 2018 Jonathan Wakely - 1.0.8a-24 - Rebuilt for Boost 1.66 * Fri Sep 22 2017 Adam Huffman - 1.0.8a-23 - rebuilt for armadillo * Thu Aug 03 2017 Fedora Release Engineering - 1.0.8a-22 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild * Wed Jul 26 2017 Fedora Release Engineering - 1.0.8a-21 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild * Mon Jul 24 2017 Björn Esser - 1.0.8a-20 - Rebuilt for Boost 1.64 * Thu Jul 13 2017 Petr Pisar - 1.0.8a-19 - perl dependency renamed to perl-interpreter * Mon May 15 2017 Fedora Release Engineering - 1.0.8a-18 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_27_Mass_Rebuild * Fri Feb 10 2017 Fedora Release Engineering - 1.0.8a-17 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild * Fri Jan 27 2017 Jonathan Wakely - 1.0.8a-16 - Rebuilt for Boost 1.63 * Thu Jun 30 2016 José Matos - 1.0.8a-15 - Rebuild for armadillo 7.x and remove BR SuperLU because armadillo takes care of that * Sat Jun 4 2016 José Matos - 1.0.8a-14 - Rebuild for armadillo 7.x * Mon May 23 2016 Jonathan Wakely - 1.0.8a-13 - Add missing BuildRequires (#1337966) * Tue May 17 2016 Jonathan Wakely - 1.0.8a-13 - Rebuilt for linker errors in boost (#1331983) * Thu Feb 25 2016 José Matos - 1.0.8a-12 - Apply the c++11 patches only to Fedora >= 24 (where g++ implements gnu++14) * Mon Feb 22 2016 Orion Poplawski - 1.0.8a-11 - Rebuild for gsl 2.1 * Fri Feb 12 2016 Adam Huffman - 1.0.8a-10 - patch to add compatibility with C++11 iostream - patch to add compatibility with C++11 static data member initialization * Wed Feb 10 2016 Adam Huffman - 1.0.8a-9 - rebuilt to pick up new armadillo * Thu Feb 04 2016 Fedora Release Engineering - 1.0.8a-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild * Fri Jan 15 2016 Jonathan Wakely - 1.0.8a-7 - Rebuilt for Boost 1.60 * Thu Aug 27 2015 Jonathan Wakely - 1.0.8a-6 - Rebuilt for Boost 1.59 * Wed Jul 29 2015 Fedora Release Engineering - 1.0.8a-5 - Rebuilt for https://fedoraproject.org/wiki/Changes/F23Boost159 * Wed Jul 22 2015 David Tardon - 1.0.8a-4 - rebuild for Boost 1.58 * Sun Jul 05 2015 Adam Huffman - 1.0.8a-3 - Update binaries and docs to install and package - Fix changelog * Wed Jun 17 2015 Fedora Release Engineering - 1.0.8a-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild * Sun Mar 01 2015 Adam Huffman - 1.0.8a-1 - Update to new Github-based upstream release - Add armadillo BR * Tue Jan 27 2015 Petr Machata - 0.9.18-14 - Rebuild for boost 1.57.0 * Sun Aug 17 2014 Fedora Release Engineering - 0.9.18-13 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild * Sat Jun 07 2014 Fedora Release Engineering - 0.9.18-12 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild * Fri May 23 2014 Petr Machata - 0.9.18-11 - Rebuild for boost 1.55.0 * Fri May 23 2014 David Tardon - 0.9.18-10 - rebuild for boost 1.55.0 * Sat Aug 03 2013 Fedora Release Engineering - 0.9.18-9 - Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild * Sat Jul 27 2013 pmachata@redhat.com - 0.9.18-8 - Rebuild for boost 1.54.0 * Thu Jul 18 2013 Petr Pisar - 0.9.18-7 - Perl 5.18 rebuild * Sun Feb 10 2013 Denis Arnaud - 0.9.18-6 - Rebuild for Boost-1.53.0 * Sat Feb 09 2013 Denis Arnaud - 0.9.18-5 - Rebuild for Boost-1.53.0 * Sun Aug 12 2012 Kevin Fenzi - 0.9.18-4 - Rebuild for new boost * Fri Jul 20 2012 Fedora Release Engineering - 0.9.18-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild * Tue Feb 28 2012 Fedora Release Engineering - 0.9.18-2 - Rebuilt for c++ ABI breakage * Wed Jan 11 2012 Adam Huffman - 0.9.18-1 - update to 0.9.18 - remove pileup.sh and get_isize.rb, discarded upstream - update patches and remove flags patch * Sun Nov 20 2011 Adam Huffman - 0.9.14-2 - rebuild for new Boost in Rawhide * Fri Oct 7 2011 Adam Huffman - 0.9.14-1 - new upstream bugfix release * Wed Aug 17 2011 Adam Huffman - 0.9.12-1 - upstream release 0.9.12 fixing a possible segfault * Thu Jul 21 2011 Adam Huffman - 0.9.11-2 - rebuild for new Boost in Rawhide * Sat May 28 2011 Adam Huffman - 0.9.11-1 - new upstream release - add routeB.sh script - sam2hits.rb removed * Fri May 27 2011 Adam Huffman - 0.9.10b-3 - patch to deal with zlib better * Sun May 15 2011 Adam Huffman - 0.9.10b-2 - remove bundled binaries - remove VERSION - explicit naming for included scripts * Sun May 8 2011 Adam Huffman - 0.9.10b-1 - new upstream version - patch descriptions * Sun May 8 2011 Adam Huffman - 0.9.9-3 - fix permissions for installed files - include missing Perl script - improve description * Sat Apr 9 2011 Adam Huffman - 0.9.9-2 - fix compilation flags for debuginfo - include shell and Ruby scripts * Mon Apr 4 2011 Adam Huffman - 0.9.9-1 - initial version