Name: bionetgen Version: 2.4.0 Release: 3%{?dist} Summary: Software for rule-based modeling of biochemical systems License: GPLv3 URL: https://github.com/RuleWorld/bionetgen Source0: https://github.com/RuleWorld/bionetgen/archive/BioNetGen-%{version}/bionetgen-BioNetGen-%{version}.tar.gz # patch based on example in # http://sundials.2283335.n4.nabble.com/Usage-notes-lead-to-the-example-that-uses-the-non-existent-header-cvode-cvode-dense-h-td4654260.html Patch0: %{name}-network-solver.patch BuildRequires: muParser-devel BuildRequires: sundials-devel BuildRequires: openmpi-devel BuildRequires: autoconf automake BuildRequires: libtool BuildRequires: gcc-c++, gcc Requires: bionetgen-perl = %{version}-%{release} # BioNetGen does not namespace its perl modules %global __provides_exclude perl\\(.*BNG.*|Cache|CartesianProduct|Compartment.*|Component.*|Console|EnergyPattern|Expression|Function|HNauty|Map|ModelWrapper|Molecule*|Observable|Param*|PatternGraph|Population*|RateLaw|RefineRule|Rxn*|SBMLMultiAux|Species*|Visualization*|XML::*|XMLReader\\) %global __requires_exclude perl\\(.*BNG.*|Cache|CartesianProduct|Compartment.*|Component.*|Console|EnergyPattern|Expression|Function|HNauty|Map|ModelWrapper|Molecule*|Observable|Param*|PatternGraph|Population*|RateLaw|RefineRule|Rxn*|SBMLMultiAux|Species*|Visualization*|XML::*|XMLReader\\) %description BioNetGen is software for the specification and simulation of rule-based models of biochemical systems, including signal transduction, metabolic, and genetic regulatory networks. The BioNetGen language has recently been extended to include explicit representation of compartments. A review of methods for rule-based modeling is available in Science Signaling (Sci. STKE, 18 July 2006, Issue 344, p. re6). BioNetGen is presently a mixture of Perl and C++. Network generation is currently implemented in Perl, the network simulator is C++, and a new language parser is being developed with ANTLR. %package perl Summary: Perl scripts used by bionetgen BuildArch: noarch BuildRequires: perl-generators Requires: bionetgen = %{version}-%{release} Requires: perl(:MODULE_COMPAT_%(eval "`%{__perl} -V:version`"; echo $version)) %description perl %{summary}. %prep %setup -q -n bionetgen-BioNetGen-%{version} # This patch must be used for Sundials 3.x %if 0%{?fedora} %autopatch -p1 %endif rm bng2/libsource/* pushd bng2/Network3 sed -i 's/AC_PROG_LIBTOOL/AM_PROG_AR\nLT_INIT/' configure.ac sed -i 's/cvode-.*//; s/muparser_.*//' configure.ac Makefile.am sed -i -r 's/(run_network_LDADD =).*/\1 libmathutils.la -lmuparser -lsundials_nvecserial -lsundials_cvode/' src/Makefile.am %build pushd bng2/Network3 autoreconf -iv %{_openmpi_load} warnings="-Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized" CXXFLAGS="%{optflags} $warnings" %configure %make_build -C src %{_openmpi_unload} popd %install %make_install -C bng2/Network3/src mkdir -vp %{buildroot}%{perl_vendorlib}/BioNetGen cp -r bng2/Perl2 %{buildroot}%{perl_vendorlib}/BioNetGen/ cp bng2/BNG2.pl %{buildroot}%{perl_vendorlib}/BioNetGen/ %files %license LICENSE %doc README.md bng2/CREDITS.txt bng2/CHANGES.txt bng2/VERSION %{_bindir}/run_network %files perl %{perl_vendorlib}/BioNetGen %changelog * Mon Nov 26 2018 Orion Poplawski - 2.4.0-3 - Rebuild for openmpi 4.0 * Fri Nov 09 2018 Antonio Trande - 2.4.0-2 - Filtering of SBMLMultiAux module * Thu Nov 08 2018 Antonio Trande - 2.4.0-1 - Release 2.4.0 - Drop obsolete patch - Rebuild on epel7 (rhbz#1647989) * Thu Jul 12 2018 Fedora Release Engineering - 2.3.0-9 - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild * Thu Jun 28 2018 Jitka Plesnikova - 2.3.0-8 - Perl 5.28 rebuild * Wed Feb 07 2018 Fedora Release Engineering - 2.3.0-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild * Wed Nov 08 2017 Antonio Trande - 2.3.0-6 - Rebuild for sundials-3.0.0 * Wed Aug 02 2017 Fedora Release Engineering - 2.3.0-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild * Wed Jul 26 2017 Fedora Release Engineering - 2.3.0-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild * Sun Jun 04 2017 Jitka Plesnikova - 2.3.0-3 - Perl 5.26 rebuild * Mon May 15 2017 Fedora Release Engineering - 2.3.0-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_27_Mass_Rebuild * Sun May 07 2017 Antonio Trande - 2.3.0-1 - Update to 2.3.0 * Wed Mar 08 2017 Antonio Trande - 2.2.6-7 - Rebuild for sundials-2.7.0-10 * Fri Feb 10 2017 Fedora Release Engineering - 2.2.6-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild * Fri Nov 04 2016 Zbigniew Jędrzejewski-Szmek - 2.2.6-5 - Rebuild for sundials-2.7.0-7 * Tue Oct 25 2016 Zbigniew Jędrzejewski-Szmek - 2.2.6-4 - Rebuild for sundials-2.7.0-6 * Sun Oct 16 2016 Zbigniew Jędrzejewski-Szmek - 2.2.6-3 - Rebuild for libsundials (#1384636) * Sun May 15 2016 Jitka Plesnikova - 2.2.6-2 - Perl 5.24 rebuild * Thu Feb 11 2016 Zbigniew Jędrzejewski-Szmek - 2.2.6-1 - Update to latest version - Fix gcc6 compilation issue (#1306648) * Wed Feb 03 2016 Fedora Release Engineering - 2.2.5-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild * Wed Jun 17 2015 Fedora Release Engineering - 2.2.5-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild * Fri Jun 05 2015 Jitka Plesnikova - 2.2.5-6 - Perl 5.22 rebuild * Sat May 02 2015 Kalev Lember - 2.2.5-5 - Rebuilt for GCC 5 C++11 ABI change * Tue Mar 31 2015 Zbigniew Jędrzejewski-Szmek - 2.2.5-4 - Rebuilt for sundials 2.6.0. * Thu Feb 26 2015 Zbigniew Jędrzejewski-Szmek - 2.2.5-3 - Rebuilt for https://fedoraproject.org/wiki/Changes/GCC5 (#1195309) * Sun Nov 30 2014 Zbigniew Jędrzejewski-Szmek - 2.2.5-2 - Drop dependency on compat f77, it is not needed. * Fri Nov 21 2014 Zbigniew Jędrzejewski-Szmek - 2.2.5-1 - Initial packaging.