66 lines
2.1 KiB
RPMSpec
66 lines
2.1 KiB
RPMSpec
Name: cufflinks
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Version: 2.2.1
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Release: 1
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Summary: Transcriptome assembly and differential expression analysis for RNA-Seq.
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License: GPL-3.0-only and BSL-1.0
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URL: http://cole-trapnell-lab.github.io/%{name}/
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Source0: https://github.com/cole-trapnell-lab/%{name}/archive/refs/tags/%{name}-%{version}.tar.gz
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Patch0: 0001-fix_spelling.patch
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Patch1: 0002-fix_includes_path.patch
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Patch2: 0003-fix_boost_tr1_path.patch
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Patch3: 0004-return_with_novalue.patch
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Patch4: 0005-fix_no_hash_member.patch
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Patch5: 0006-format-security.patch
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Patch6: 0007-py2to3.patch
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Patch7: 0008-boost_bind_header.patch
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BuildRequires: boost boost-serialization boost-system boost-thread boost-devel samtools samtools-devel htslib htslib-devel
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BuildRequires: gcc gcc-c++ gcc-gfortran make autoconf gmp mpfr openmpi java-1.8.0-openjdk-headless
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BuildRequires: python3 ncurses-devel eigen3-devel xz-devel bzip2-devel zlib-devel
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Recommends: gffread
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%description
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Cufflinks assembles transcripts, estimates their abundances, and tests for
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differential expression and regulation in RNA-Seq samples. It accepts aligned
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RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts.
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Cufflinks then estimates the relative abundances of these transcripts based on
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how many reads support each one, taking into account biases in library
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preparation protocols.
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%prep
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%autosetup -p1
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%build
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autoreconf --install >/dev/null 2>&1
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if ! ./configure \
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--prefix=%{_prefix} \
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%ifarch aarch64
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--build=arm \
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%endif
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--with-boost --with-eigen --with-bam \
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LIBS="-lboost_system -lboost_thread -lboost_serialization" \
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PYTHON="$(command -v python3)"; then
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: cat log
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cat config.log
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fi
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%make_build CXXFLAGS="-I/usr/include/eigen3 -lhts -L%{_libdir} -lpthread"
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%install
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%make_install
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# skip gffread binary provided by gffread package
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find %{buildroot}/%{_bindir}/ -type f -name gffread -delete
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%files
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%license LICENSE
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%doc README AUTHORS doc
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%{_bindir}/*
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%changelog
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* Wed Mar 24 2021 He Rengui <herengui@uniontech.com> - 2.2.1-1
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- Package init
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