File gbench.spec of Package gbench

#
# spec file for package gbench
#
# Copyright (c) 2012 Matthias Mailänder
# Copyright (c) 2022 SUSE LLC
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
# upon. The license for this file, and modifications and additions to the
# file, is the same license as for the pristine package itself (unless the
# license for the pristine package is not an Open Source License, in which
# case the license is the MIT License). An "Open Source License" is a
# license that conforms to the Open Source Definition (Version 1.9)
# published by the Open Source Initiative.

# Please submit bugfixes or comments via https://bugs.opensuse.org/
#


Name:           gbench
Version:        3.8.1
Release:        0
Summary:        View and analyze genome sequences
Group:          Productivity/Scientific/Other
License:        SUSE-Public-Domain
URL:            https://www.ncbi.nlm.nih.gov/tools/gbench/
Source0:        https://ftp.ncbi.nlm.nih.gov/toolbox/gbench/ver-%{version}/gbench-src-%{version}.tar.gz
# PATCH-FIX-OPENSUSE -- fix broken MFLAGS mangling, causing quadratic -jN behavior
Patch0:         fix_MFLAGS.patch
# PATCH-FIX-OPENSUSE -- fix broken GDK_DISPLAY call
Patch1:         fix_GDK_DISPLAY_call.patch
# PATCH-FIX-OPENSUSE -- remove call to removed wxSearchCtrl::IsModified
Patch2:         0001-Trigger-changed-event-on-leave-events.patch
# PATCH-FIX-OPENSUSE -- Add missing conversion for wxUSE_STL builds
Patch3:         0001-Fix-missing-conversion-from-wxString-to-std-string.patch
BuildRequires:  fdupes
BuildRequires:  fltk-devel
BuildRequires:  freeglut-devel
BuildRequires:  freetds-devel
BuildRequires:  freetype2-devel
BuildRequires:  ftgl-devel
BuildRequires:  gcc-c++
BuildRequires:  giflib-devel
BuildRequires:  gl2ps-devel
BuildRequires:  glew-devel
BuildRequires:  hdf5-devel
BuildRequires:  libboost_chrono-devel > 1.35
BuildRequires:  libboost_filesystem-devel
BuildRequires:  libboost_iostreams-devel
BuildRequires:  libboost_regex-devel
BuildRequires:  libboost_program_options-devel
BuildRequires:  libboost_serialization-devel
BuildRequires:  libboost_system-devel
BuildRequires:  libboost_test-devel
BuildRequires:  libboost_thread-devel
BuildRequires:  libcurl-devel
BuildRequires:  libcppunit-devel
BuildRequires:  libexpat-devel
BuildRequires:  libgnutls-devel
BuildRequires:  libicu-devel
BuildRequires:  libjpeg-devel
BuildRequires:  libmysqlclient-devel
BuildRequires:  libnghttp2-devel
BuildRequires:  libpng12-devel
BuildRequires:  libtiff-devel
BuildRequires:  libuv-devel
BuildRequires:  libxalan-c-devel
BuildRequires:  libxerces-c-devel
BuildRequires:  libxml2-devel
BuildRequires:  libxslt-devel
BuildRequires:  libdb-4_8-devel
BuildRequires:  lzo-devel
BuildRequires:  muparser-devel
BuildRequires:  ncbi-vdb-devel
BuildRequires:  pcre-devel
BuildRequires:  python3-devel
BuildRequires:  sablot-devel
BuildRequires:  sed
BuildRequires:  sqlite3-devel
BuildRequires:  update-desktop-files
# Several incompatibilities between gbench and GTK3
BuildRequires:  wxWidgets-devel >= 3.1
#BuildRequires:  wxGTK3-devel >= 3.1
BuildRequires:  zlib-devel

%description
NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data.
Genome Workbench was developed entirely in-house at NCBI and makes use of the NCBI C++ ToolKit.
The C++ ToolKit provides a convenient and flexible cross-platform API for managing system internals,
database connections, network sockets, and the NCBI data model. In addition, the C++ ToolKit
provides the Object Manager, which abstracts handling of sequences and sequence-related objects.

%prep
%setup
%autopatch -p1

%build
%global optflags %{optflags} -Wno-error=return-type
# Add mising GTK+-2.0 include dir
export CXXFLAGS="%{optflags} `pkg-config gtk+-2.0 --cflags-only-I` "
# Make reproducible
export NCBI_BUILD_SESSION_ID=${SOURCE_DATE_EPOCH}
# Missing lib dependencies
sed -i -e '/DLL_LIB/ s/.*/\0 w_data/' src/gui/widgets/text_widget/Makefile.w_text_widget.lib
sed -i -e '/DLL_LIB/ s/.*/\0 fastme/' src/algo/phy_tree/Makefile.xalgophytree.lib

# with-3psw enables preference of system packages
./configure \
  --target=%{_target_platform} \
  --prefix=%{_prefix} \
  --exec-prefix=%{_exec_prefix} \
  --with-mt \
  --with-gbench \
  --with-3psw \
  --with-libxml \
  --with-libxslt \
  --without-sse42 \
  --with-wxwidgets-ucs \
  --without-debug \
  --with-vdb=%{_includedir}/ncbi-vdb \
  --with-projects=scripts/projects/ncbi_gbench.lst \
  --with-runpath="%{_libdir}/gbench/lib" \
  --without-sybase \
  --with-flat-makefile \
  --without-caution \
  --with-build-root="build"

%make_build

%install
cd build/build/app/gbench/gbench_install
make install_dir=%{buildroot}%{_libdir}/gbench

%suse_update_desktop_file -c gbench GBench "NCBI Genome Workbench" "%{_libdir}/gbench/bin/gbench-bin" "%{_libdir}/gbench/share/gbench/gbench_about.png" Education Science

# Remove unneeded wrapper script
rm %{buildroot}%{_libdir}/gbench/bin/gbench
mkdir  %{buildroot}%{_bindir}
ln -s %{_libdir}/gbench/bin/gbench-bin %{buildroot}%{_bindir}/gbench
# brp RPATH check is broken, and has been removed post 15.4
export NO_BRP_CHECK_RPATH=true

%fdupes %{buildroot}/%{_libdir}/gbench

%post -p /sbin/ldconfig
%postun -p /sbin/ldconfig

%files
%{_bindir}/gbench
%{_datadir}/applications/*
%dir %{_libdir}/gbench
%dir %{_libdir}/gbench/lib/
%dir %{_libdir}/gbench/share/
%dir %{_libdir}/gbench/packages/
%{_libdir}/gbench/bin
%{_libdir}/gbench/etc
%{_libdir}/gbench/lib/lib*.so
%{_libdir}/gbench/share/gbench
%{_libdir}/gbench/packages/alignment
%{_libdir}/gbench/packages/sequence
%{_libdir}/gbench/packages/sequence_edit
%{_libdir}/gbench/packages/snp

%changelog