163 lines
4.7 KiB
RPMSpec
163 lines
4.7 KiB
RPMSpec
Name: mmseq
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Version: 1.0.8a
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Release: 1%{?dist}
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Summary: Haplotype and isoform specific expression estimation for RNA-seq
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Group: Applications/Engineering
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License: GPLv2+
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URL: https://github.com/eturro/%{name}
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Source0: https://github.com/eturro/%{name}/archive/%{version}.zip
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Patch0: mmseq-sam-header.patch
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#Patch1: mmseq-flags.patch
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Patch2: mmseq-zlib.patch
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BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
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BuildRequires: boost-devel
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BuildRequires: samtools-devel
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BuildRequires: gsl-devel
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BuildRequires: zlib-devel
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Requires: ruby
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Requires: samtools
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Requires: perl
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%description
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Software for fast, scalable haplotype and isoform expression
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estimation using multi-mapping RNA-seq reads. Example scripts are included.
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%prep
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%setup -q -n %{name}-%{version}
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#Look for samtools headers in the correct location for Fedora
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%patch0 -p1 -b .mmseq-sam-header.patch
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#Use Fedora compilation headers
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#%%patch1 -p1 -b .mmseq-flags.patch
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#Fix zlib linking
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%patch2 -p1 -b .mmseq-zlib.patch
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#Remove bundled binaries
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rm bam2hits*-x86_64
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rm mmseq*-x86_64
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%build
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make %{?_smp_mflags} CXXFLAGS="%{optflags}"
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%install
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rm -rf %{buildroot}
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mkdir -p %{buildroot}%{_bindir}
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install -p -m 0755 bam2hits %{buildroot}%{_bindir}
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install -p -m 0755 mmseq %{buildroot}%{_bindir}
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install -p -m 0755 *.sh %{buildroot}%{_bindir}
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install -p -m 0755 *.rb %{buildroot}%{_bindir}
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install -p -m 0755 ensembl_gtf_to_gff.pl %{buildroot}%{_bindir}
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%clean
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rm -rf %{buildroot}
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%files
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%defattr(-,root,root,-)
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%doc AUTHORS COPYING
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%{_bindir}/bam2hits
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%{_bindir}/mmseq
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%{_bindir}/fastagrep.sh
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#%%{_bindir}/pileup.sh
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%{_bindir}/routeB.sh
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%{_bindir}/filterGTF.rb
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#%%{_bindir}/get_isize.rb
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%{_bindir}/haploref.rb
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%{_bindir}/testregexp.rb
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%{_bindir}/ensembl_gtf_to_gff.pl
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%changelog
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* Sun Mar 01 2015 Adam Huffman <bloch@verdurin.com> - 1.0.8a
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- Update to new Github-based upstream release
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* Tue Jan 27 2015 Petr Machata <pmachata@redhat.com> - 0.9.18-14
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- Rebuild for boost 1.57.0
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* Sun Aug 17 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.9.18-13
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild
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* Sat Jun 07 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.9.18-12
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild
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* Fri May 23 2014 Petr Machata <pmachata@redhat.com> - 0.9.18-11
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- Rebuild for boost 1.55.0
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* Fri May 23 2014 David Tardon <dtardon@redhat.com> - 0.9.18-10
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- rebuild for boost 1.55.0
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* Sat Aug 03 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.9.18-9
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild
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* Sat Jul 27 2013 pmachata@redhat.com - 0.9.18-8
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- Rebuild for boost 1.54.0
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* Thu Jul 18 2013 Petr Pisar <ppisar@redhat.com> - 0.9.18-7
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- Perl 5.18 rebuild
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* Sun Feb 10 2013 Denis Arnaud <denis.arnaud_fedora@m4x.org> - 0.9.18-6
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- Rebuild for Boost-1.53.0
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* Sat Feb 09 2013 Denis Arnaud <denis.arnaud_fedora@m4x.org> - 0.9.18-5
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- Rebuild for Boost-1.53.0
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* Sun Aug 12 2012 Kevin Fenzi <kevin@scrye.com> - 0.9.18-4
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- Rebuild for new boost
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* Fri Jul 20 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.9.18-3
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild
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* Tue Feb 28 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.9.18-2
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- Rebuilt for c++ ABI breakage
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* Wed Jan 11 2012 Adam Huffman <verdurin@fedoraproject.org> - 0.9.18-1
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- update to 0.9.18
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- remove pileup.sh and get_isize.rb, discarded upstream
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- update patches and remove flags patch
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* Sun Nov 20 2011 Adam Huffman <adam@vaioz.verdurin.salon> - 0.9.14-2
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- rebuild for new Boost in Rawhide
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* Fri Oct 7 2011 Adam Huffman <bloch@verdurin.com> - 0.9.14-1
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- new upstream bugfix release
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* Wed Aug 17 2011 Adam Huffman <bloch@verdurin.com> - 0.9.12-1
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- upstream release 0.9.12 fixing a possible segfault
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* Thu Jul 21 2011 Adam Huffman <bloch@verdurin.com> - 0.9.11-2
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- rebuild for new Boost in Rawhide
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* Sat May 28 2011 Adam Huffman <bloch@verdurin.com> - 0.9.11-1
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- new upstream release
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- add routeB.sh script
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- sam2hits.rb removed
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* Fri May 27 2011 Adam Huffman <bloch@verdurin.com> - 0.9.10b-3
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- patch to deal with zlib better
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* Sun May 15 2011 Adam Huffman <bloch@verdurin.com> - 0.9.10b-2
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- remove bundled binaries
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- remove VERSION
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- explicit naming for included scripts
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* Sun May 8 2011 Adam Huffman <bloch@verdurin.com> - 0.9.10b-1
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- new upstream version
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- patch descriptions
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* Sun May 8 2011 Adam Huffman <bloch@verdurin.com> - 0.9.9-3
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- fix permissions for installed files
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- include missing Perl script
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- improve description
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* Sat Apr 9 2011 Adam Huffman <bloch@verdurin.com> - 0.9.9-2
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- fix compilation flags for debuginfo
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- include shell and Ruby scripts
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* Mon Apr 4 2011 Adam Huffman <bloch@verdurin.com> - 0.9.9-1
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- initial version
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