Name:           ray
Version:        2.1.0
Release:        2%{?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/Ray-v%{version}.tar.bz2

BuildRequires:  openmpi-devel, bzip2-devel, zlib-devel, mpich2-devel
BuildRequires:  help2man

%description
Ray is a parallel software that computes de novo genome assemblies with   
next-generation sequencing data.
Ray is written in C++ and can run in parallel on numerous interconnected 
computers using the message-passing interface (MPI) standard.
Included:
 - Ray de novo assembly of single genomes
 - Ray Méta de novo assembly of metagenomes
 - Ray Communities microbe abundance + taxonomic profiling
 - Ray Ontologies gene ontology profiling

%package common
Summary:        Parallel genome assemblies for parallel DNA sequencing
Group:          Applications/Engineering

%description common
Ray is a parallel software that computes de novo genome assemblies with   
next-generation sequencing data.
Ray is written in C++ and can run in parallel on numerous interconnected 
computers using the message-passing interface (MPI) standard.

%package openmpi
Summary:        Ray package for Open-MPI
Group:          Applications/Engineering
Requires:       openmpi, ray-common

%description openmpi
Ray is a parallel software that computes de novo genome assemblies with   
next-generation sequencing data.
Ray is written in C++ and can run in parallel on numerous interconnected 
computers using the message-passing interface (MPI) standard.

%package mpich2
Summary:        Ray package for MPICH2
Group:          Applications/Engineering
Requires:       mpich2, ray-common

%description mpich2
Ray is a parallel software that computes de novo genome assemblies with   
next-generation sequencing data.
Ray is written in C++ and can run in parallel on numerous interconnected 
computers using the message-passing interface (MPI) standard.

%package doc
Summary:        Documentation files
Group:          Documentation
Requires:       ray-common

%description doc
Ray is a parallel software that computes de novo genome assemblies with   
next-generation sequencing data.
Ray is written in C++ and can run in parallel on numerous interconnected 
computers using the message-passing interface (MPI) standard.

%package extra
Summary:        Scripts and XSL sheets for post-processing
Group:          Applications/Engineering
Requires:       python, R, ray-common

%description extra
Ray is a parallel software that computes de novo genome assemblies with   
next-generation sequencing data.
Ray is written in C++ and can run in parallel on numerous interconnected 
computers using the message-passing interface (MPI) standard.

%prep
%setup -q -n Ray-v%{version}

%build
CXXFLAGS="%{optflags} -D MAXKMERLENGTH=32 -D HAVE_LIBZ -D HAVE_LIBBZ2 -D "
CXXFLAGS+="RAY_VERSION=\\\\\\\"2.1.0\\\\\\\" "
CXXFLAGS+="-D RAYPLATFORM_VERSION=\\\\\\\"1.1.0\\\\\\\" -I . -I ../RayPlatform"

%{_openmpi_load}
make CXXFLAGS="$CXXFLAGS" HAVE_LIBBZ2=y HAVE_LIBZ=y
cp Ray Ray$MPI_SUFFIX

pwd

# generate the man page with Ray --help
# rsh agent is not available in chroot (mock) !
export OMPI_MCA_orte_rsh_agent=/bin/false
help2man --no-info --help-option=--help -o Ray.1.man \
  -n "assemble genomes in parallel using the message-passing interface" \
  ./Ray

# remove symbols that are not in U.S. American English 
sed 's/Erdős.*Rényi/Erdos-Renyi/g;s/é/e/g;s/É/E/g;s/ç/c/g;s/ő/o/g' \
  Ray.1.man > Ray.1

rm Ray.1.man

make clean
%{_openmpi_unload}

%{_mpich2_load}
make CXXFLAGS="$CXXFLAGS" HAVE_LIBBZ2=y HAVE_LIBZ=y
cp Ray Ray$MPI_SUFFIX
make clean
%{_mpich2_unload}

%install
rm -rf %{buildroot}

# ray-common
mkdir -p %{buildroot}%{_mandir}/man1
install -m 0644 Ray.1 %{buildroot}%{_mandir}/man1/Ray.1

# ray-openmpi
%{_openmpi_load}
mkdir -p %{buildroot}$MPI_BIN
install -m 0755 Ray$MPI_SUFFIX %{buildroot}$MPI_BIN
%{_openmpi_unload}

# ray-mpich2
%{_mpich2_load}
mkdir -p %{buildroot}$MPI_BIN
install -m 0755 Ray$MPI_SUFFIX %{buildroot}$MPI_BIN
%{_mpich2_unload}

# ray-doc
mkdir doc
cp -ar RayPlatform/Documentation/ doc/RayPlatform
chmod 644 doc/RayPlatform/*
chmod 644 Documentation/*

# ray-extra
mkdir -p %{buildroot}%{_datadir}/ray
cp -r scripts %{buildroot}%{_datadir}/ray
chmod 0755 %{buildroot}%{_datadir}/ray/scripts

%clean
rm -rf %{buildroot}

%files common
%doc MANUAL_PAGE.txt gpl-3.0.txt LICENSE.txt 
%doc RayPlatform/lgpl-3.0.txt README.md
%{_mandir}/man1/Ray.1*

%files openmpi
%{_libdir}/openmpi/bin/Ray*

%files mpich2
%{_libdir}/mpich2/bin/Ray*

%files doc
%doc Documentation/*
%doc doc/RayPlatform/

%files extra
%{_datadir}/ray/

%changelog

* Fri Nov 4 2012 Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca> - 2.1.0-2
- Added build dependency help2man 
- Added OMPI_MCA_orte_rsh_agent to pass mock builds

* Fri Nov 3 2012 Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca> - 2.1.0-1

- The Spec file was (informally) reviewed by Jussi Lehtola
- Moved subpackage declarations to the top
- Added subpackages 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