File VarGibbs.spec of Package VarGibbs
#
# spec file for package [VarGibbs]
#
# norootforbuild
Name: VarGibbs
Version: 2.2
Release: 1.0.0
#Release: 1.<CI_CNT>.<B_CNT>
Summary: Calculation of DNA nearest-neighbour thermodynamic parameters
License: GPL-3.0
Group: Productivity/Scientific/Physics
URL: https://sites.google.com/site/geraldweberufmg/vargibbs
Source0: vargibbs-2.2.tar.bz2
BuildRequires: gcc-c++
BuildRequires: gsl gsl-devel
BuildRequires: boost-devel
%if 0%{?suse_version} == 1310
BuildRequires: libboost_filesystem1_53_0 libboost_system1_53_0 libboost_iostreams1_53_0
%endif
%if 0%{?suse_version} == 1320
BuildRequires: libboost_filesystem1_54_0 libboost_system1_54_0 libboost_iostreams1_54_0
%endif
#OpenSuSE Leap 15.0
%if 0%{?suse_version} == 1500
BuildRequires: libboost_filesystem1_66_0-devel libboost_system1_66_0-devel libboost_regex1_66_0-devel libboost_iostreams1_66_0-devel
%endif
#OpenSuSE Tumbleweed as of 03/2019
%if 0%{?suse_version} == 1550
BuildRequires: libboost_filesystem1_69_0-devel libboost_system1_69_0-devel libboost_regex1_69_0-devel libboost_iostreams1_69_0-devel
%endif
%if %{defined fedora}
BuildRequires: boost-filesystem
%endif
%if 0%{?suse_version}
BuildRequires: libblas3
%endif
%if %{defined fedora}
BuildRequires: blas
%endif
BuildRequires: zlib-devel
#specific script for dealing with file duplicates
%if ! %{defined scientificlinux_version} && ! %{defined centos_version} && ! %{defined rhel}
BuildRequires: fdupes
%endif
%description
Numerical method for calculating nearest-neighbour (NN) entropy and enthalpy parameters
from nucleotide melting temperatures.
%prep
%setup -q
%build
make
%install
mkdir -p %{buildroot}/%{_bindir}
install -m 755 vargibbs %{buildroot}/%{_bindir}/vargibbs
mkdir -p %{buildroot}/%{_datadir}/%{name}
cp -r examples %{buildroot}/%{_datadir}/%{name}
cp -r data %{buildroot}/%{_datadir}/%{name}
%if ! %{defined scientificlinux_version} && ! %{defined centos_version} && ! %{defined rhel}
%fdupes -s %{buildroot}/%{_datadir}
%endif
%clean
rm -rf %%{buildroot}
%files
%defattr(-, root, root)
%{_bindir}/vargibbs
%doc doc/vargibbs-user-manual.pdf
%doc gpl-3.0.txt
%{_datadir}/%{name}
%changelog
* Fri Mar 22 2019 <gweberbh@gmail.com> 2.2
New parameter files for hybrid DNA-RNA. New option to require log files to be written in gzip format (new option -zlog). Redesign of NN calculation taking advantage of pointers, CPU times reduce by a factor of 7 compared to previous versions. Added symmetry_correction_entropy to some parameter files. New parameter file P-SL04.par. boost_iostreams library is now required for compilation.
* Fri Oct 05 2018 <gweberbh@gmail.com> 2.1
New parameters for RNA with salt dependence. New option for performing numerous salt corrections.
* Fri Aug 25 2017 <gweberbh@gmail.com> 2.0
Modifications for hybrid DNA-RNA sequences with specific naming scheme for parameters. Documentation updates and corrections. Corrected parameter files P-BS86.par and P-FR86.par for RNA.
Several new parameters from the literature. Added new option nnpo for using NN parameters only.
* Thu Dec 10 2015 <gweberbh@gmail.com> 1.1
Documentation updates. Code clean up, removed gbc_exp from C++ name space. Linking to the library libboost_regex is now required. Added optimized parameter files at different salt concentrations for D-OW04 datasets. Added new parameters from the literature. Correcting bug which was not generating complementary sequence when cseq was not given. You can now specify a list of Ct concentrations in option -ct.
* Fri Jul 25 2014 <gweberbh@gmail.com> 1.0
First Public Release
