178 lines
5.3 KiB
RPMSpec
178 lines
5.3 KiB
RPMSpec
Name: seqan
|
|
Summary: Open source C++ library of efficient algorithms and data structures
|
|
Version: 1.4.2
|
|
Release: 8%{?dist}
|
|
License: BSD and GPLv3+ and LGPLv3+
|
|
URL: http://www.seqan.de/
|
|
Source0: http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz
|
|
|
|
## This patch sets a seqan directory for documentation files
|
|
Patch0: %{name}-docpath.patch
|
|
|
|
## These patches exclude tests of splazers, fiona, bs_tools
|
|
## They fail beacause unknown reasons
|
|
Patch1: %{name}-exclude_splazers_fiona_tests.patch
|
|
Patch2: %{name}-exclude_bstools_test.patch
|
|
|
|
BuildRequires: qt4-devel >= 4.7
|
|
BuildRequires: cmake >= 2.8
|
|
BuildRequires: llvm-devel, bzip2-devel, zlib-devel, boost-devel
|
|
BuildRequires: coin-or-lemon-devel, openmpi-devel, libstdc++-static
|
|
|
|
## Test
|
|
BuildRequires: python2-devel, python-nose, pytest, python-jinja2
|
|
|
|
%if 0%{?fedora} < 21
|
|
BuildRequires: java-1.7.0-openjdk-devel
|
|
%else
|
|
BuildRequires: java-1.8.0-openjdk-devel
|
|
%endif
|
|
|
|
Requires: gawk
|
|
|
|
## Bundled files exception https://fedorahosted.org/fpc/ticket/174
|
|
Provides: bundled(gnulib)
|
|
|
|
%description
|
|
SeqAn is an open source C++ library of efficient algorithms and data structures
|
|
for the analysis of sequences with the focus on biological data.
|
|
Our library applies a unique generic design that guarantees high performance,
|
|
generality, extensibility, and integration with other libraries.
|
|
|
|
%package devel
|
|
Summary: SeqAn development files
|
|
|
|
%description devel
|
|
Developer files for SeqAn, in the form for C header files.
|
|
|
|
%package doc
|
|
Summary: SeqAn documentation
|
|
BuildArch: noarch
|
|
Requires: %{name}
|
|
|
|
%description doc
|
|
Info files of SeqAn's apps.
|
|
|
|
%prep
|
|
%setup -q -n seqan-%{version}
|
|
%patch0 -p0
|
|
%patch1 -p0
|
|
|
|
%ifarch %{arm}
|
|
%patch2 -p0
|
|
%endif
|
|
|
|
## Remove spurious executable permissions
|
|
for i in `find . -perm /111 -type f \( -name "*.h" -o -name "*.cpp" \)`; do
|
|
chmod a-x $i
|
|
done
|
|
|
|
## Renamed each single license file
|
|
cp -p extras/apps/rep_sep/LICENSE LGPLv3+.txt
|
|
cp -p core/apps/rabema/LICENSE GPLv3+.txt
|
|
cp -p LICENSE BSD.txt
|
|
|
|
## Make install needs this README file
|
|
cp -p extras/apps/seqan_flexbar/INFO extras/apps/seqan_flexbar/README
|
|
|
|
%build
|
|
mkdir -p build/Release && pushd build/Release
|
|
cmake \
|
|
-DCMAKE_C_FLAGS_RELEASE:STRING="$RPM_OPT_FLAGS" \
|
|
-DCMAKE_CXX_FLAGS_RELEASE:STRING="$RPM_OPT_FLAGS" \
|
|
-DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} \
|
|
-DSYSCONF_INSTALL_DIR:PATH=%{_sysconfdir} \
|
|
-DSHARE_INSTALL_PREFIX:PATH=%{_datadir} \
|
|
-DBUILD_SHARED_LIBS:BOOL=OFF \
|
|
-DCMAKE_BUILD_TYPE:STRING=Release -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS \
|
|
-DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_APP_VERSION:STRING=%{version} \
|
|
-DZLIB_INCLUDE_DIR:PATH=%{_includedir} -DZLIB_LIBRARY:FILEPATH="-L%{_libdir} -lz" \
|
|
-DBZIP2_INCLUDE_DIR:PATH=%{_includedir} -DBZIP2_LIBRARY:FILEPATH="-L%{_libdir} -lbz2" \
|
|
-DLEMON_INCLUDE_DIR:PATH=%{_includedir} -DLEMON_LIBRARY:FILEPATH="-L%{_libdir} -lemon" \
|
|
-DBoost_INCLUDE_DIR:PATH=%{_includedir} \
|
|
-DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE \
|
|
../..
|
|
|
|
%ifarch %{arm}
|
|
make all
|
|
%else
|
|
make %{?_smp_mflags} all
|
|
%endif
|
|
|
|
%install
|
|
%make_install -C build/Release INSTALL="install -p"
|
|
|
|
## Put header files in ad-hoc include directory
|
|
mkdir -p %{buildroot}%{_includedir}/seqan
|
|
cp -pr extras/include/seqan/* %{buildroot}%{_includedir}/seqan
|
|
cp -pr core/include/seqan/* %{buildroot}%{_includedir}/seqan
|
|
|
|
## Rename 'join' binary file; it conflicts with the one owned by 'coreutils' package
|
|
mv %{buildroot}%{_bindir}/join %{buildroot}%{_bindir}/searchjoin
|
|
|
|
## Fix executable permissions
|
|
for i in `find %{buildroot}%{_bindir} -perm /644 -type f \( -name "*.sh" \)`; do
|
|
chmod a+x $i
|
|
done
|
|
|
|
%check
|
|
pushd build/Release
|
|
%ifarch %{arm}
|
|
ctest --force-new-ctest-process
|
|
%else
|
|
ctest --force-new-ctest-process %{?_smp_mflags}
|
|
%endif
|
|
|
|
%files
|
|
%doc BSD.txt GPLv3+.txt LGPLv3+.txt README.rst
|
|
%{_bindir}/*
|
|
|
|
%files doc
|
|
%doc %{_docdir}/seqan
|
|
|
|
%files devel
|
|
%doc BSD.txt GPLv3+.txt LGPLv3+.txt README.rst
|
|
%{_includedir}/seqan/
|
|
|
|
%changelog
|
|
* Tue Dec 02 2014 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-8
|
|
- Excluded bs_tools test on ARM
|
|
|
|
* Mon Dec 01 2014 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-7
|
|
- Parallel tests not performed on ARM
|
|
|
|
* Mon Dec 01 2014 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-6
|
|
- DBUILD_SHARED_LIBS boolean disabled
|
|
- Test enabled
|
|
|
|
* Tue Nov 25 2014 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-5
|
|
- Parallel make excluded on ARM arch
|
|
|
|
* Tue Nov 25 2014 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-4
|
|
- Tests disabled temporarily
|
|
|
|
* Sat Nov 22 2014 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-3
|
|
- Packaged private libraries
|
|
- Performed tests
|
|
- Splazers and fiona tests excluded
|
|
|
|
* Sat Nov 22 2014 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-2
|
|
- Parallel make excluded on ARM arch
|
|
|
|
* Fri Nov 21 2014 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-1
|
|
- Update to 1.4.2
|
|
- Fixed cmake compiler flags
|
|
- Fixed declaration of multiple license
|
|
- A doc sub-package is now built
|
|
|
|
* Mon Aug 18 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.4.1-3
|
|
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild
|
|
|
|
* Sat Jun 14 2014 Antonio Trande <sagitterATfedoraproject.org> 1.4.1-2
|
|
- Added 'Provides:bundled(gnulib)'
|
|
- Changed find command for executable permissions fixing
|
|
- Use %%make_install
|
|
- Fixed wrong-file-end-of-line-encoding warnings
|
|
|
|
* Wed Jun 11 2014 Antonio Trande <sagitterATfedoraproject.org> 1.4.1-1
|
|
- First package
|