[bionetgen] Initial packaging

[Zbigniew Jędrzejewski-Szmek]

commit 0c95a23617e8338ec13547a60bb51029855bccc0
Author: Zbigniew Jędrzejewski-Szmek <zbyszek at in.waw.pl>
Date:   Fri Nov 21 19:19:39 2014 -0500

    Initial packaging
    
    No perl so far.

 bionetgen.spec |   56 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 sources        |    1 +
 2 files changed, 57 insertions(+), 0 deletions(-)
---
diff --git a/bionetgen.spec b/bionetgen.spec
new file mode 100644
index 0000000..418adb7
--- /dev/null
+++ b/bionetgen.spec
@@ -0,0 +1,56 @@
+Name:           bionetgen
+Version:        2.2.5
+Release:        1%{?dist}
+Summary:        Software for rule-based modeling of biochemical systems
+
+License:        GPLv3
+URL:            https://code.google.com/p/bionetgen/
+Source0:        https://bionetgen.googlecode.com/files/BioNetGen-%{version}-stable.zip
+
+BuildRequires:  compat-gcc-34-g77
+BuildRequires:  muParser-devel
+BuildRequires:  sundials-devel
+BuildRequires:  openmpi-devel
+BuildRequires:  autoconf automake
+
+%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.
+
+%prep
+%setup -q -n BioNetGen-%{version}-stable
+pushd Network3
+sed -i 's/AC_PROG_LIBTOOL/AM_PROG_AR\n\0/' configure.ac
+sed -i 's/cvode-2\.6\.0//; s/muparser_v2_2_3//' configure.ac Makefile.am
+sed -i -r 's/(run_network_LDADD =).*/\1 libmathutils.la -lmuparser -lsundials_nvecserial -lsundials_cvode/' src/Makefile.am
+rm -rf Network3/cvode-2.6.0 Network3/muparser_v2_2_3
+
+%build
+pushd Network3
+autoreconf -iv
+%_openmpi_load
+
+%configure
+make %{?_smp_mflags}
+
+%install
+pushd Network3
+%make_install
+
+%files
+%license LICENSE.txt
+%doc CREDITS.txt CHANGES.txt README_FIRST.txt
+%{_bindir}/run_network
+
+%changelog
+* Fri Nov 21 2014 Zbigniew Jędrzejewski-Szmek <zbyszek at in.waw.pl> - 2.2.5-1
+- Initial packaging.
diff --git a/sources b/sources
index e69de29..d68b6f6 100644
--- a/sources
+++ b/sources
@@ -0,0 +1 @@
+673176aa28f581f2ac268b5aecdefde1  BioNetGen-2.2.5-stable.zip