From 0aabc542d721ab30ebbd9a07d52015247f8623d1 Mon Sep 17 00:00:00 2001 From: sagitter Date: Feb 11 2018 16:16:30 +0000 Subject: Compile pyOpenMS --- diff --git a/openms.spec b/openms.spec index 15d50db..ef9babc 100644 --- a/openms.spec +++ b/openms.spec @@ -1,12 +1,12 @@ -%global with_py2OpenMS 0 -%global with_py3OpenMS 0 +%global with_py2OpenMS 1 +%global with_py3OpenMS 1 %global with_check 0 Name: openms Summary: LC/MS data management and analyses Version: 2.3.0 -Release: 6%{?dist} +Release: 7%{?dist} License: BSD URL: http://www.openms.de/ Source0: https://github.com/OpenMS/OpenMS/archive/Release%{version}.tar.gz#/OpenMS-Release%{version}.tar.gz @@ -27,6 +27,7 @@ BuildRequires: coin-or-Clp-devel BuildRequires: coin-or-CoinUtils-devel BuildRequires: coin-or-Osi-devel BuildRequires: libsvm-devel +BuildRequires: gcc-c++ BuildRequires: gsl-devel BuildRequires: glpk-devel BuildRequires: xerces-c-devel @@ -40,6 +41,7 @@ BuildRequires: tbb-devel BuildRequires: eigen3-devel BuildRequires: desktop-file-utils BuildRequires: fido-pi +BuildRequires: percolator BuildRequires: libappstream-glib ## Build documentation @@ -51,6 +53,7 @@ BuildRequires: texlive, texlive-a4wide, texlive-xtab BuildRequires: xorg-x11-server-Xvfb, gnuplot Requires: fido-pi%{?_isa} +Requires: percolator%{?_isa} Requires: R-core%{?_isa} Requires: %{name}-data%{?_isa} = %{version}-%{release} @@ -76,8 +79,8 @@ including label-free quantitation, SILAC, iTRAQ, SRM, SWATH, etc. It provides built-in algorithms for de-novo identification and database search, as well as adapters to other state-of-the art tools like XTandem, Mascot, OMSSA, etc. -It supports easy integration of OpenMS built tools into workflow engines like Knime, -Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept and +It supports easy integration of OpenMS built tools into workflow engines like +Knime, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept and a unified parameter handling via a 'common tool description' (CTD) scheme. The OpenMS Proteomics Pipeline is a pipeline for @@ -125,14 +128,15 @@ The UTILS tools are divided into several subgroups: Summary: OpenMS Python2 bindings %{?python_provide:%python_provide python2-%{name}} -BuildRequires: python-setuptools +BuildRequires: python2-setuptools BuildRequires: python2-devel -BuildRequires: numpy -BuildRequires: python-nose +BuildRequires: python2-numpy +BuildRequires: python2-nose BuildRequires: python2-autowrap >= 0.8.0 -BuildRequires: Cython, python-wheel -BuildRequires: python-biopython -Requires: python-biopython%{?_isa} +BuildRequires: python2-Cython +BuildRequires: python2-wheel +BuildRequires: python2-biopython +Requires: python2-biopython%{?_isa} Requires: %{name}-data%{?_isa} = %{version}-%{release} Requires: %{name}%{?_isa} = %{version}-%{release} @@ -227,9 +231,10 @@ export LDFLAGS="%{__global_ldflags} -Wl,-z,now -Wl,--as-needed" -DCMAKE_CXX_FLAGS_RELEASE:STRING="-Wno-cpp $RPM_OPT_FLAGS -Wl,-z,relro -Wl,-z,now" -DCMAKE_C_FLAGS_RELEASE:STRING="-Wno-cpp $RPM_OPT_FLAGS -Wl,-z,relro -Wl,-z,now " \ -DCMAKE_VERBOSE_MAKEFILE=TRUE -DCMAKE_PREFIX_PATH=%{_prefix} \ -DENABLE_SVN=OFF -DCMAKE_BUILD_TYPE=Release -DBOOST_USE_STATIC=OFF \ - -DCMAKE_SKIP_RPATH:BOOL=TRUE -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES \ + -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=NO \ -DMT_ENABLE_OPENMP=ON -DENABLE_GCC_WERROR:BOOL=OFF \ -DFIDO_BINARY:FILEPATH=%{_bindir}/Fido -DFIDOCHOOSEPARAMS_BINARY:FILEPATH=%{_bindir}/FidoChooseParameters \ + -DPERCOLATOR_BINARY:FILEPATH=%{_bindir}/percolator \ -DBOOST_USE_STATIC:BOOL=OFF -DBoost_INCLUDE_DIR:PATH=%{_includedir} \ -DBoost_IOSTREAMS_LIBRARY_RELEASE:FILEPATH=%{_libdir}/libboost_iostreams.so \ -DBoost_MATH_C99_LIBRARY_RELEASE:FILEPATH=%{_libdir}/libboost_math_c99.so \ @@ -284,9 +289,10 @@ export LDFLAGS="%{__global_ldflags} -Wl,-z,now -Wl,--as-needed" -DCMAKE_CXX_FLAGS_RELEASE:STRING="-Wno-cpp $RPM_OPT_FLAGS -Wl,-z,relro -Wl,-z,now" -DCMAKE_C_FLAGS_RELEASE:STRING="-Wno-cpp $RPM_OPT_FLAGS -Wl,-z,relro -Wl,-z,now " \ -DCMAKE_VERBOSE_MAKEFILE=TRUE -DCMAKE_PREFIX_PATH=%{_prefix} \ -DENABLE_SVN=OFF -DCMAKE_BUILD_TYPE=Release -DBOOST_USE_STATIC=OFF \ - -DCMAKE_SKIP_RPATH:BOOL=TRUE -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES \ + -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=NO \ -DMT_ENABLE_OPENMP=ON -DENABLE_GCC_WERROR:BOOL=OFF \ -DFIDO_BINARY:FILEPATH=%{_bindir}/Fido -DFIDOCHOOSEPARAMS_BINARY:FILEPATH=%{_bindir}/FidoChooseParameters \ + -DPERCOLATOR_BINARY:FILEPATH=%{_bindir}/percolator \ -DBOOST_USE_STATIC:BOOL=OFF -DBoost_INCLUDE_DIR:PATH=%{_includedir} \ -DBoost_IOSTREAMS_LIBRARY_RELEASE:FILEPATH=%{_libdir}/libboost_iostreams.so \ -DBoost_MATH_C99_LIBRARY_RELEASE:FILEPATH=%{_libdir}/libboost_math_c99.so \ @@ -330,12 +336,8 @@ xvfb-run -a make install DESTDIR=%{buildroot} cd pyOpenMS %{__python2} setup.py install --skip-build --root %{buildroot} -ln -s -f %{_libdir}/OpenMS/libOpenMS.so %{buildroot}%{python2_sitearch}/pyopenms/libOpenMS.so -ln -s -f %{_libdir}/OpenMS/libOpenSwathAlgo.so %{buildroot}%{python2_sitearch}/pyopenms/libOpenSwathAlgo.so -ln -s -f %{_libdir}/OpenMS/libSuperHirn.so %{buildroot}%{python2_sitearch}/pyopenms/libSuperHirn.so - ## Fix standard permissions -chmod 0755 %{buildroot}%{python2_sitearch}/pyopenms/pyopenms.so +chmod 0755 %{buildroot}%{python2_sitearch}/pyopenms/*.so cd .. %endif popd @@ -347,10 +349,6 @@ xvfb-run -a make install DESTDIR=%{buildroot} cd pyOpenMS %{__python3} setup.py install --skip-build --root %{buildroot} - -ln -s -f %{_libdir}/OpenMS/libOpenMS.so %{buildroot}%{python3_sitearch}/pyopenms/libOpenMS.so -ln -s -f %{_libdir}/OpenMS/libOpenSwathAlgo.so %{buildroot}%{python3_sitearch}/pyopenms/libOpenSwathAlgo.so -ln -s -f %{_libdir}/OpenMS/libSuperHirn.so %{buildroot}%{python3_sitearch}/pyopenms/libSuperHirn.so cd .. popd %endif @@ -507,6 +505,7 @@ xvfb-run -a ctest -V -R OpenMS_ --force-new-ctest-process %{?_smp_mflags} %{_bindir}/MetaboliteSpectralMatcher %{_bindir}/OpenSwathWorkflow %{_bindir}/PeakPickerIterative +%{_bindir}/PercolatorAdapter %{_bindir}/SimpleSearchEngine %{_bindir}/IDScoreSwitcher %{_bindir}/MzMLSplitter @@ -521,7 +520,6 @@ xvfb-run -a ctest -V -R OpenMS_ --force-new-ctest-process %{?_smp_mflags} %{_libdir}/OpenMS/ %files tools -%{_bindir}/PercolatorAdapter %{_bindir}/CometAdapter %{_bindir}/MetaboliteAdductDecharger %{_bindir}/OpenPepXL @@ -586,6 +584,8 @@ xvfb-run -a ctest -V -R OpenMS_ --force-new-ctest-process %{?_smp_mflags} %doc py2build/CHANGELOG py2build/AUTHORS py2build/README %license py2build/LICENSE %{_datadir}/OpenMS/ +%exclude %{_datadir}/OpenMS/examples/external_code/*.h +%exclude %{_datadir}/OpenMS/examples/external_code/*.cpp %files doc %doc py2build/CHANGELOG py2build/AUTHORS py2build/README @@ -596,6 +596,8 @@ xvfb-run -a ctest -V -R OpenMS_ --force-new-ctest-process %{?_smp_mflags} %license py2build/LICENSE %doc py2build/CHANGELOG py2build/AUTHORS py2build/README %{_includedir}/OpenMS/ +%{_datadir}/OpenMS/examples/external_code/*.h +%{_datadir}/OpenMS/examples/external_code/*.cpp %if 0%{?with_py2OpenMS} %files -n python2-openms @@ -612,6 +614,11 @@ xvfb-run -a ctest -V -R OpenMS_ --force-new-ctest-process %{?_smp_mflags} %endif %changelog +* Sun Feb 11 2018 Antonio Trande - 2.3.0-7 +- Compile pyOpenMS +- Set Python2 required packages +- Disable rpaths skipping + * Thu Feb 08 2018 Fedora Release Engineering - 2.3.0-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild