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# Smoldyn provides the SFMT-1.3.3 (SIMD-oriented Fast Mersenne Twister) source code;
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# currently unavailable on Fedora.
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# http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/index.html
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%global with_libs 0
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00ff2c8 |
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# VTK support?
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# See https://github.com/ssandrews/Smoldyn-official/issues/3
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00ff2c8 |
%global with_vtk 0
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00ff2c8 |
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00ff2c8 |
Name: smoldyn
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00ff2c8 |
Summary: A particle-based spatial stochastic simulator
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00ff2c8 |
Version: 2.58
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00ff2c8 |
Release: 1%{?dist}
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00ff2c8 |
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# The rxnparam.c and SurfaceParam.c source code files are in the public domain.
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#
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# The Next Subvolume module is Copyright 2012 by Martin Robinson and is distributed
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# under the Gnu LGPL license.
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00ff2c8 |
#
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# The rest of the code is Copyright 2003-2018 by Steven Andrews and also
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00ff2c8 |
# distributed under the Gnu LGPL.
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00ff2c8 |
#
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00ff2c8 |
# source/lib/SFMT is licensed under the 'BSD 3-clause "New" or "Revised" License'
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License: LGPLv3+ and Public Domain and BSD
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00ff2c8 |
URL: http://www.smoldyn.org
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00ff2c8 |
Source0: %{url}/%{name}-%{version}.tgz
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00ff2c8 |
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00ff2c8 |
# Fix library paths according to the Fedora Project guidelines
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00ff2c8 |
Patch0: %{name}-fix_libpaths.patch
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00ff2c8 |
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00ff2c8 |
BuildRequires: boost-devel
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00ff2c8 |
BuildRequires: cmake3
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00ff2c8 |
BuildRequires: gcc
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00ff2c8 |
BuildRequires: %{?dts}gcc-c++
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00ff2c8 |
%if 0%{?rhel} == 7
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00ff2c8 |
BuildRequires: devtoolset-7-toolchain, devtoolset-7-libatomic-devel
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00ff2c8 |
# Coming on epel7
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00ff2c8 |
#BuildRequires: boost169-devel
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00ff2c8 |
%endif
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00ff2c8 |
BuildRequires: freeglut-devel
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00ff2c8 |
BuildRequires: libXmu-devel
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00ff2c8 |
BuildRequires: libXi-devel
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00ff2c8 |
BuildRequires: libtiff-devel
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00ff2c8 |
BuildRequires: libglvnd-devel
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00ff2c8 |
%if %{?with_vtk}
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00ff2c8 |
BuildRequires: vtk-devel
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00ff2c8 |
%endif
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00ff2c8 |
BuildRequires: zlib-devel
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00ff2c8 |
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00ff2c8 |
Requires: bionetgen-perl
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00ff2c8 |
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00ff2c8 |
Provides: bundled(SFMT) = 1.3.3
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00ff2c8 |
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00ff2c8 |
%description
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00ff2c8 |
Smoldyn is a computer program for cell-scale biochemical simulations.
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00ff2c8 |
It simulates each molecule of interest individually to capture natural
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00ff2c8 |
stochasticity and to yield nanometer-scale spatial resolution.
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00ff2c8 |
It treats other molecules implicitly, enabling it to simulate hundreds
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00ff2c8 |
of thousands of molecules over several minutes of real time.
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00ff2c8 |
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00ff2c8 |
Simulated molecules diffuse, react, are confined by surfaces,
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00ff2c8 |
and bind to membranes much as they would in a real biological system.
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00ff2c8 |
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00ff2c8 |
It is more accurate and faster than other particle-based simulators.
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00ff2c8 |
Smoldyn's unique features include: a "virtual experimenter" who can
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00ff2c8 |
manipulate or measure the simulated system, support for spatial compartments,
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00ff2c8 |
molecules with excluded volume, and simulations in 1, 2, or 3 dimensions.
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00ff2c8 |
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00ff2c8 |
%if %{?with_libs}
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00ff2c8 |
%package devel
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00ff2c8 |
Summary: %{name} devel files
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00ff2c8 |
Requires: %{name}%{?_isa} = %{version}-%{release}
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00ff2c8 |
Provides: %{name}-static = %{version}-%{release}
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00ff2c8 |
%description devel
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00ff2c8 |
This package provides the %{name} examples, header files and private libraries.
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00ff2c8 |
%endif
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00ff2c8 |
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00ff2c8 |
%package doc
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00ff2c8 |
Summary: %{name} PDF documentation
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00ff2c8 |
Requires: %{name} = %{version}-%{release}
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00ff2c8 |
BuildArch: noarch
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00ff2c8 |
%description doc
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00ff2c8 |
%{name} PDF documentation.
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00ff2c8 |
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00ff2c8 |
%prep
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00ff2c8 |
%setup -q -n %{name}-%{version}
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00ff2c8 |
%patch0 -p0 -b .fix_libpaths
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00ff2c8 |
|
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00ff2c8 |
# Copy license file
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00ff2c8 |
mv source/lib/SFMT/LICENSE.txt source/lib/SFMT/SFMT-LICENSE.txt
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00ff2c8 |
mv source/lib/SFMT/README.txt source/lib/SFMT/SFMT-README.txt
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00ff2c8 |
|
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00ff2c8 |
# Remove pre-built archives
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|
00ff2c8 |
rm -rf Linux
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00ff2c8 |
|
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00ff2c8 |
# Remove bundled libraries
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|
00ff2c8 |
rm -rf source/BioNetGen source/MinGWlibs Toolchain-mingw32.cmake
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00ff2c8 |
rm -rf source/vcell/* source/NextSubVolume/Eigen
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|
00ff2c8 |
rm -rf source/NextSubVolume/boost_include
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00ff2c8 |
%if !%{?with_vtk}
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00ff2c8 |
rm -f source/vtk/*
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00ff2c8 |
%endif
|
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|
00ff2c8 |
|
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00ff2c8 |
#Fix permissions
|
|
|
00ff2c8 |
find . -type f -name "*.h" -exec chmod 0644 '{}' \;
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|
00ff2c8 |
find . -type f -name "*.c" -exec chmod 0644 '{}' \;
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|
00ff2c8 |
find . -type f -name "*.pdf" -exec chmod 0644 '{}' \;
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|
00ff2c8 |
find . -type f -name "*.txt" -exec chmod 0644 '{}' \;
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|
00ff2c8 |
find . -type f -name "*.txt" -exec sed -i 's/\r$//' '{}' \;
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00ff2c8 |
|
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|
00ff2c8 |
# Set system path to BNG2.pl
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|
00ff2c8 |
sed -e 's|../../../source/BioNetGen/BNG2.pl|%{perl_vendorlib}/BioNetGen/BNG2.pl|g' -i examples/S95_regression/lrmsim.txt \
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|
00ff2c8 |
examples/S12_bionetgen/lrm/lrmsim.txt \
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|
00ff2c8 |
examples/S12_bionetgen/abba/abbasim.txt \
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|
00ff2c8 |
examples/S94_archive/Andrews_2016/BioNetGen/lrm/lrmsim.txt \
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|
00ff2c8 |
examples/S94_archive/Andrews_2016/BioNetGen/abba/abbasim.txt
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00ff2c8 |
|
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|
00ff2c8 |
%build
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00ff2c8 |
mkdir -p build && pushd build
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|
00ff2c8 |
%if 0%{?rhel} == 7
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|
00ff2c8 |
. /opt/rh/devtoolset-7/enable
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|
00ff2c8 |
%endif
|
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|
00ff2c8 |
%cmake3 -Wno-dev \
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|
|
00ff2c8 |
-DCPACK_BINARY_STGZ:BOOL=OFF \
|
|
|
00ff2c8 |
-DCPACK_BINARY_TGZ:BOOL=OFF \
|
|
|
00ff2c8 |
-DCPACK_BINARY_TZ:BOOL=OFF \
|
|
|
00ff2c8 |
-DCPACK_SOURCE_TBZ2:BOOL=OFF \
|
|
|
00ff2c8 |
-DCPACK_SOURCE_TGZ:BOOL=OFF \
|
|
|
00ff2c8 |
-DCPACK_SOURCE_TXZ:BOOL=OFF \
|
|
|
00ff2c8 |
-DCPACK_SOURCE_TZ:BOOL=OFF \
|
|
|
00ff2c8 |
-DOPTION_VCELL:BOOL=OFF \
|
|
|
00ff2c8 |
%if %{?with_vtk}
|
|
|
00ff2c8 |
-DOPTION_VTK:BOOL=ON \
|
|
|
00ff2c8 |
%else
|
|
|
00ff2c8 |
-DOPTION_VTK:BOOL=OFF \
|
|
|
00ff2c8 |
%endif
|
|
|
00ff2c8 |
%if %{?with_libs}
|
|
|
00ff2c8 |
-DOPTION_TARGET_LIBSMOLDYN:BOOL=ON \
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|
00ff2c8 |
%else
|
|
|
00ff2c8 |
-DOPTION_TARGET_LIBSMOLDYN:BOOL=OFF \
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|
|
00ff2c8 |
%endif
|
|
|
00ff2c8 |
-DOPTION_USE_ZLIB:BOOL=ON \
|
|
|
00ff2c8 |
-DOPTION_PDE:BOOL=ON \
|
|
|
00ff2c8 |
-DPERL_VENDORLIB:PATH=%{perl_vendorlib} \
|
|
|
00ff2c8 |
-DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_INSTALL_LIBDIR:PATH=%{_libdir} \
|
|
|
00ff2c8 |
-DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} \
|
|
|
00ff2c8 |
-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE -DCMAKE_COLOR_MAKEFILE:BOOL=ON \
|
|
|
00ff2c8 |
-DCMAKE_SKIP_RPATH:BOOL=YES ..
|
|
|
00ff2c8 |
%make_build V=1
|
|
|
00ff2c8 |
popd
|
|
|
00ff2c8 |
|
|
|
00ff2c8 |
%install
|
|
|
00ff2c8 |
%make_install -C build
|
|
|
00ff2c8 |
|
|
|
00ff2c8 |
%files
|
|
|
00ff2c8 |
%doc source/lib/SFMT/SFMT-README.txt
|
|
|
00ff2c8 |
%license License.txt source/lib/SFMT/SFMT-LICENSE.txt
|
|
|
00ff2c8 |
%{_bindir}/%{name}
|
|
|
00ff2c8 |
|
|
|
00ff2c8 |
%if %{?with_libs}
|
|
|
00ff2c8 |
%files devel
|
|
|
00ff2c8 |
%doc examples
|
|
|
00ff2c8 |
%{_includedir}/%{name}/
|
|
|
00ff2c8 |
%{_libdir}/%{name}/
|
|
|
00ff2c8 |
%endif
|
|
|
00ff2c8 |
|
|
|
00ff2c8 |
%files doc
|
|
|
00ff2c8 |
%doc documentation/*
|
|
|
00ff2c8 |
|
|
|
00ff2c8 |
%changelog
|
|
|
00ff2c8 |
* Fri Mar 29 2019 Antonio Trande <sagitter@fedoraproject.org> - 2.58-1
|
|
|
00ff2c8 |
- Release 2.58
|
|
|
00ff2c8 |
|
|
|
00ff2c8 |
* Sun Feb 03 2019 Antonio Trande <sagitter@fedoraproject.org> - 2.56-1
|
|
|
00ff2c8 |
- First package
|
|
|
00ff2c8 |
- Unbundle zlib, boost and BioNetGen
|
|
|
00ff2c8 |
- Remove unused header files
|
|
|
00ff2c8 |
- Fix file permissions
|
|
|
00ff2c8 |
- Add License file provided by upstream
|