%if 0%{?epel} < 7

%{!?__global_ldflags: %global __global_ldflags -Wl,-z,relro}

%endif

Name:           wise2

Version:        2.4.1

Release:        11%{?dist}

Summary:        Tools for comparison of bio-polymers

## Everything is licensed under a BSD-style license except for

## the HMMer2 libraries and models directory which are GPLv2+

## see LICENSE files for details. 

License:        BSD and GPLv2+

URL:            http://www.ebi.ac.uk/~birney/%{name}/

Source0:        http://www.ebi.ac.uk/~birney/%{name}/wise%{version}.tar.gz

## Patches from Debian package. Thanks to Philipp Benner

Patch0:         %{name}-build.patch

Patch1:         %{name}-isnumber.patch

Patch2:         %{name}-glib2.patch

Patch3:         %{name}-getline.patch

Patch4:         %{name}-ld--as-needed.patch

Patch5:         %{name}-mayhem.patch

BuildRequires: glib2-devel, gcc, perl

BuildRequires: strace

BuildRequires: pkgconfig

%description

Wise2 is a package focused on comparisons of bio-polymers, commonly DNA

sequence and protein sequence.  A strength of Wise2 is the

comparison of DNA sequence at the level of its protein

translation. This comparison allows the simultaneous prediction of

gene structure with homology based alignment.

%package doc

Summary:    Wise2 documentation

BuildArch:  noarch

%description doc

Wise2, Wise2api and Dynamite documentation files.

%package examples

Summary:    Wise2 examples

Requires:   %{name}%{?_isa} = %{version}-%{release}

%description examples

Here are some examples that you might want to try out.  The

Wise2 executables of course should be installed before.

%prep

%setup -q -n wise%{version}

%patch0 -p1

%patch1 -p1

%patch2 -p1

%patch3 -p1

%patch4 -p1

# Remove spurious-executable-perm

chmod a-x src/external/mott/mott_api.c

chmod a-x src/external/mott/mott_api.h

chmod a-x src/external/mott/gaplib.c

chmod a-x src/external/mott/gapstat.h

## fix interpreter in examples

sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' docs/gettex.pl

## fix perms 

chmod -x test_data/rrm.HMM

## pull out licenses

for i in base dynlibsrc dyc

do

    cp src/$i/LICENSE LICENSE.$i

done

cp src/models/GNULICENSE LICENSE.GPL

%build

## removed "{?_smp_mflags}", does not support parallel build

export LDFLAGS="%{__global_ldflags}"

make -C src CC=gcc \

 CFLAGS=" -c $RPM_OPT_FLAGS -pthread -D_GNU_SOURCE %(pkg-config --cflags glib-2.0) -D_POSIX_C_SOURCE=200112L" all

%install

pushd src/bin

mkdir -p $RPM_BUILD_ROOT%{_bindir}

for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb

do

    install -pm 755 $i $RPM_BUILD_ROOT%{_bindir} 

done

popd

# install architecture-independent data and config files

mkdir -p $RPM_BUILD_ROOT%{_datadir}/wise2

pushd wisecfg

install -pm 644 * $RPM_BUILD_ROOT%{_datadir}/wise2

popd

# install architecture-independent files to run example tests

mkdir -p $RPM_BUILD_ROOT%{_datadir}/wise2/examples

pushd test_data

install -pm 644 * $RPM_BUILD_ROOT%{_datadir}/wise2/examples

popd

# install scripts to automatically set the WISECONFIGDIR environment variable

mkdir -p $RPM_BUILD_ROOT%{_sysconfdir}/profile.d

echo "export WISECONFIGDIR=%{_datadir}/wise2/" > $RPM_BUILD_ROOT%{_sysconfdir}/profile.d/wise2.sh

echo "setenv WISECONFIGDIR %{_datadir}/wise2/" > $RPM_BUILD_ROOT%{_sysconfdir}/profile.d/wise2.csh

%check

export WISECONFIGDIR=$PWD/wisecfg

make -C src test

%files

%doc README

%license LICENSE LICENSE.base LICENSE.dynlibsrc LICENSE.dyc LICENSE.GPL

%{_bindir}/genewisedb

%{_bindir}/estwisedb

%{_bindir}/genewise

%{_bindir}/estwise

%{_bindir}/scanwise

%{_bindir}/promoterwise

%{_bindir}/pswdb

%{_bindir}/dba

%{_bindir}/psw

%{_bindir}/scanwise_server

%{_bindir}/dnal

%{_datadir}/wise2/

%config(noreplace) %{_sysconfdir}/profile.d/*

%files doc

%license LICENSE

%doc docs

%files examples

%doc test_data/README

%{_datadir}/wise2/examples/

%changelog

* Wed Jul 29 2020 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-11

- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild

* Fri Jan 31 2020 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-10

- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild

* Sat Jul 27 2019 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-9

- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild

* Sun Feb 03 2019 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-8

- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild

* Sat Jul 14 2018 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-7

- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild

* Thu Feb 22 2018 Antonio Trande <sagitter@fedoraproject.org> - 2.4.1-6

- Add gcc perl BR

* Fri Feb 09 2018 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-5

- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild

* Thu Aug 03 2017 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-4

- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild

* Thu Jul 27 2017 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-3

- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild

* Sat Feb 11 2017 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-2

- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild

* Tue May 05 2015 Antonio Trande <sagitterATfedoraproject.org> - 2.4.1-1

- Update to 2.4.1

- Fix compiler flags

* Sun Aug 04 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.2.0-12

- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild

* Fri Feb 15 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.2.0-11

- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild

* Sun Jul 22 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.2.0-10

- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild

* Sat Jan 14 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.2.0-9

- Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild

* Mon Feb 07 2011 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.2.0-8

- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild

* Mon Jul 27 2009 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.2.0-7

- Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild

* Thu Jul 16 2009 Alex Lancaster <alexlan[AT]fedoraproject org> - 2.2.0-6

- Add -D_POSIX_C_SOURCE=200112L to CFLAGS as a workaround to fix FTBFS (#511627)

* Wed Feb 25 2009 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.2.0-5

- Rebuilt for https://fedoraproject.org/wiki/Fedora_11_Mass_Rebuild

* Sat Feb  9 2008 Alex Lancaster <alexlan[AT]fedoraproject org> - 2.2.0-4

- rebuilt for GCC 4.3 as requested by Fedora Release Engineering

* Thu Aug 16 2007 Alex Lancaster <alexl@users.sourceforge.net> 2.2.0-3

- Clarify license as BSD and GPLv2+

* Thu Apr 12 2007 Alex Lancaster <alexl@users.sourceforge.net> 2.2.0-2

- Pass $RPM_OPT_FLAGS to compiler as per suggestion from Ralf Corsepius.

* Wed Apr 11 2007 Alex Lancaster <alexl@users.sourceforge.net> 2.2.0-1

- Initial Fedora package.