Name: Ray Version: 2.3.1 Release: 21%{?dist} Summary: Parallel genome assemblies for parallel DNA sequencing Group: Applications/Engineering License: GPLv3 URL: http://denovoassembler.sourceforge.net/ Source0: http://downloads.sourceforge.net/denovoassembler/%{name}-%{version}.tar.bz2 Patch0: Ray.manpage.patch Patch1: pthread.patch %global useMpich 1 %ifarch ppc64 %if 0%{?rhel}==5 || 0%{?rhel} == 6 %global useMpich 0 %endif %endif # el5 still uses the old name MPICH2 %if 0%{?rhel}==5 %global mpichName mpich2 %else %global mpichName mpich %endif BuildRequires: gcc-c++ BuildRequires: openmpi-devel BuildRequires: bzip2-devel BuildRequires: zlib-devel %if %useMpich BuildRequires: %{mpichName}-devel %endif %description %{name} is a parallel software that computes de novo genome assemblies with next-generation sequencing data. %{name} is written in C++ and can run in parallel on numerous interconnected computers using the message-passing interface (MPI) standard. Included: - %{name} de novo assembly of single genomes - %{name} Méta de novo assembly of metagenomes - %{name} Communities microbe abundance + taxonomic profiling - %{name} Ontologies gene ontology profiling %package common Summary: Parallel genome assemblies for parallel DNA sequencing Group: Applications/Engineering %description common %{name} is a parallel software that computes de novo genome assemblies with next-generation sequencing data. %{name} is written in C++ and can run in parallel on numerous interconnected computers using the message-passing interface (MPI) standard. This sub-package contains common files for Ray. %package openmpi Summary: %{name} package for Open-MPI Group: Applications/Engineering Requires: %{name}-common %description openmpi %{name} is a parallel software that computes de novo genome assemblies with next-generation sequencing data. %{name} is written in C++ and can run in parallel on numerous interconnected computers using the message-passing interface (MPI) standard. This sub-package enables parallel computation using openmpi. %if %useMpich %package %{mpichName} Summary: %{name} package for MPICH Group: Applications/Engineering Requires: %{name}-common %if %{mpichName} == "mpich" Obsoletes: %{name}-mpich2 < 2.3.1-4 Conflicts: %{name}-mpich2 < 2.3.1-4 %endif %description %{mpichName} %{name} is a parallel software that computes de novo genome assemblies with next-generation sequencing data. %{name} is written in C++ and can run in parallel on numerous interconnected computers using the message-passing interface (MPI) standard. This sub-package enables parallel computation using mpich. %endif %package doc Summary: Documentation files Group: Documentation Requires: %{name}-common %description doc %{name} is a parallel software that computes de novo genome assemblies with next-generation sequencing data. %{name} is written in C++ and can run in parallel on numerous interconnected computers using the message-passing interface (MPI) standard. This sub-package includes documentation files. %package extra Summary: Scripts and XSL sheets for post-processing Group: Applications/Engineering Requires: python2, R, %{name}-common %description extra %{name} is a parallel software that computes de novo genome assemblies with next-generation sequencing data. %{name} is written in C++ and can run in parallel on numerous interconnected computers using the message-passing interface (MPI) standard. This sub-package contains scripts and XSL sheets for post-processing. %prep %setup -q -n %{name}-%{version} %patch0 %patch1 %build CXXFLAGS="%{optflags}" %{_openmpi_load} make CXXFLAGS="$CXXFLAGS" HAVE_LIBBZ2=y HAVE_LIBZ=y Q= cp %{name} %{name}$MPI_SUFFIX cp README.md README cp %{name}Platform/README.md README.%{name}Platform cp %{name}Platform/AUTHORS AUTHORS.%{name}Platform make clean %{_openmpi_unload} %if %useMpich # %{_%{mpichName}_load} does not work %if %mpichName == "mpich" %{_mpich_load} %else %{_mpich2_load} %endif make CXXFLAGS="$CXXFLAGS" HAVE_LIBBZ2=y HAVE_LIBZ=y Q= cp %{name} %{name}$MPI_SUFFIX make clean %if %mpichName == "mpich" %{_mpich_unload} %else %{_mpich2_unload} %endif %endif %install rm -rf %{buildroot} # Ray-common mkdir -p %{buildroot}%{_mandir}/man1 install -m 0644 %{name}.1 %{buildroot}%{_mandir}/man1/%{name}.1 # Ray-openmpi %{_openmpi_load} mkdir -p %{buildroot}$MPI_BIN install -m 0755 %{name}$MPI_SUFFIX %{buildroot}$MPI_BIN %{_openmpi_unload} %if %useMpich # Ray-mpich %if %mpichName == "mpich" %{_mpich_load} %else %{_mpich2_load} %endif mkdir -p %{buildroot}$MPI_BIN install -m 0755 %{name}$MPI_SUFFIX %{buildroot}$MPI_BIN %if %mpichName == "mpich" %{_mpich_unload} %else %{_mpich2_unload} %endif %endif # Ray-doc mkdir doc cp -ar %{name}Platform/Documentation/ doc/%{name}Platform chmod 644 doc/%{name}Platform/* chmod 644 Documentation/* # Ray-extra mkdir -p %{buildroot}%{_datadir}/%{name} cp -r scripts %{buildroot}%{_datadir}/%{name} chmod 0755 %{buildroot}%{_datadir}/%{name}/scripts %files common %doc MANUAL_PAGE.txt gpl-3.0.txt LICENSE.txt %doc %{name}Platform/lgpl-3.0.txt %doc AUTHORS AUTHORS.%{name}Platform %doc README README.%{name}Platform %{_mandir}/man1/%{name}.1* %files openmpi %{_libdir}/openmpi/bin/%{name}* %if %useMpich %files %{mpichName} %{_libdir}/%{mpichName}/bin/%{name}* %endif %files doc %doc Documentation/* %doc doc/%{name}Platform/ %files extra %{_datadir}/%{name}/ %changelog * Mon Nov 26 2018 Orion Poplawski - 2.3.1-21 - Rebuild for openmpi 4.0 * Thu Jul 12 2018 Fedora Release Engineering - 2.3.1-20 - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild * Mon Mar 26 2018 Iryna Shcherbina - 2.3.1-19 - Update Python 2 dependency declarations to new packaging standards (See https://fedoraproject.org/wiki/FinalizingFedoraSwitchtoPython3) * Wed Feb 07 2018 Fedora Release Engineering - 2.3.1-18 - Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild * Wed Aug 02 2017 Fedora Release Engineering - 2.3.1-17 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild * Wed Jul 26 2017 Fedora Release Engineering - 2.3.1-16 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild * Fri Feb 10 2017 Fedora Release Engineering - 2.3.1-15 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild * Fri Oct 21 2016 Orion Poplawski - 2.3.1-14 - Rebuild for openmpi 2.0 * Wed Feb 03 2016 Fedora Release Engineering - 2.3.1-13 - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild * Tue Sep 15 2015 Orion Poplawski - 2.3.1-12 - Rebuild for openmpi 1.10.0 * Sat Aug 15 2015 Zbigniew Jędrzejewski-Szmek - 2.3.1-11 - Rebuild for MPI provides * Sun Jul 26 2015 Sandro Mani - 2.3.1-10 - Rebuild for RPM MPI Requires Provides Change * Tue Jun 16 2015 Fedora Release Engineering - 2.3.1-9 - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild * Sat May 02 2015 Kalev Lember - 2.3.1-8 - Rebuilt for GCC 5 C++11 ABI change * Mon Mar 16 2015 Sebastien Boisvert - 2.3.1-7 - fix linking issue in rawhide * Wed Nov 5 2014 Tuomo Soini - 2.3.1-6 - Ray-mpich2 got obsoleted by rhel 6.6 update * Fri Aug 15 2014 Fedora Release Engineering - 2.3.1-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild * Fri Jun 06 2014 Fedora Release Engineering - 2.3.1-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild * Sun Mar 2 2014 Sébastien Boisvert - 2.3.1-3 - use correct macro name to load/unload mpich2 * Mon Feb 24 2014 Sébastien Boisvert - 2.3.1-2 - add a variable for mpich package name (mpich or mpich2) * Mon Feb 24 2014 Sébastien Boisvert - 2.3.1-1 - Fix days of week in spec changelog (rpmlint warning) - Update version with upstream. * Wed Sep 04 2013 Sébastien Boisvert - 2.1.0-8 - Change dependency name from mpich2 to mpich * Fri Aug 02 2013 Fedora Release Engineering - 2.1.0-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild * Mon Jul 15 2013 Sébastien Boisvert - 2.1.0-6 - Skip mpich2 on el5 and el6 for ppc64 * Thu Nov 29 2012 Sébastien Boisvert - 2.1.0-5 - Added a patch for the man page * Mon Nov 5 2012 Sébastien Boisvert - 2.1.0-4 - The man page encoding is en_US.UTF-8 - Added more specific descriptions * Sun Nov 4 2012 Sébastien Boisvert - 2.1.0-3 - Changed the package name from ray to Ray - Renamed README.md to README - Added AUTHORS, README.RayPlatform, AUTHORS.RayPlatform * Sun Nov 4 2012 Sébastien Boisvert - 2.1.0-2 - Added build dependency help2man - Added OMPI_MCA_orte_rsh_agent to pass mock builds * Sat Nov 3 2012 Sébastien Boisvert - 2.1.0-1 - The Spec file was (informally) reviewed by Jussi Lehtola - Moved sub-package declarations to the top - Added sub-packages common, openmpi, mpich2 - Removed useless '/' after buildroot - Fixed the packaging of Documentation - Removed symbols that are not U.S. American English from man page - Added Fedora compilation flags (optflags) - The Spec file was (informally) reviewed a second time by Jussi Lehtola - CXXFLAGS was shortened - Replacement of non-ASCII symbols is more compact with sed - ray-extra now ships _datadir/ray/ instead of _datadir/ray/scripts/. - This is the initial Ray package for Fedora