# Generated from protk-1.4.4.gem by gem2rpm -*- rpm-spec -*-
%global gem_name protk

Name: rubygem-%{gem_name}
Version: 1.4.4
Release: 1%{?dist}
Summary: Proteomics Toolkit
License: LGPL-2.1
URL: http://rubygems.org/gems/protk
Source0: https://rubygems.org/gems/%{gem_name}-%{version}.gem
BuildRequires: ruby(release)
BuildRequires: rubygems-devel
BuildRequires: ruby-devel
# Compiler is required for build of gem binary extension.
# https://fedoraproject.org/wiki/Packaging:C_and_C++#BuildRequires_and_Requires
BuildRequires: gcc
# BuildRequires: rubygem(rspec) >= 3.0
# BuildRequires: rubygem(rspec) < 4
# BuildRequires: rubygem(rspec-mocks) >= 3.0
# BuildRequires: rubygem(rspec-mocks) < 4
# BuildRequires: rubygem(rake-compiler)
# BuildRequires: rubygem(rake-compiler) < 1
# BuildRequires: rubygem(byebug) >= 3.5
# BuildRequires: rubygem(byebug) < 4

%description
Commandline tools for proteomics.


%package doc
Summary: Documentation for %{name}
Requires: %{name} = %{version}-%{release}
BuildArch: noarch

%description doc
Documentation for %{name}.

%prep
%setup -q -n %{gem_name}-%{version}

%build
# Create the gem as gem install only works on a gem file
gem build ../%{gem_name}-%{version}.gemspec

# %%gem_install compiles any C extensions and installs the gem into ./%%gem_dir
# by default, so that we can move it into the buildroot in %%install
%gem_install

%install
mkdir -p %{buildroot}%{gem_dir}
cp -a .%{gem_dir}/* \
        %{buildroot}%{gem_dir}/

mkdir -p %{buildroot}%{gem_extdir_mri}
cp -a .%{gem_extdir_mri}/{gem.build_complete,*.so} %{buildroot}%{gem_extdir_mri}/

# Prevent dangling symlink in -debuginfo (rhbz#878863).
rm -rf %{buildroot}%{gem_instdir}/ext/

mkdir -p %{buildroot}%{_bindir}
cp -a .%{_bindir}/* \
        %{buildroot}%{_bindir}/

find %{buildroot}%{gem_instdir}/bin -type f | xargs chmod a+x

%check
pushd .%{gem_instdir}
# rspec spec
popd

%files
%dir %{gem_instdir}
%{_bindir}/protk_setup.rb
%{_bindir}/manage_db.rb
%{_bindir}/tandem_search.rb
%{_bindir}/mascot_search.rb
%{_bindir}/omssa_search.rb
%{_bindir}/msgfplus_search.rb
%{_bindir}/mascot_to_pepxml.rb
%{_bindir}/tandem_to_pepxml.rb
%{_bindir}/make_decoy.rb
%{_bindir}/repair_run_summary.rb
%{_bindir}/add_retention_times.rb
%{_bindir}/peptide_prophet.rb
%{_bindir}/interprophet.rb
%{_bindir}/protein_prophet.rb
%{_bindir}/pepxml_to_table.rb
%{_bindir}/unimod_to_loc.rb
%{_bindir}/uniprot_mapper.rb
%{_bindir}/sixframe.rb
%{_bindir}/augustus_to_proteindb.rb
%{_bindir}/maker_to_proteindb.rb
%{_bindir}/protxml_to_gff.rb
%{_bindir}/protxml_to_table.rb
%{_bindir}/swissprot_to_table.rb
%{_bindir}/protxml_to_psql.rb
%{_bindir}/mzid_to_protxml.rb
%{_bindir}/mzid_to_pepxml.rb
%{_bindir}/spectrast_create.rb
%{_bindir}/spectrast_filter.rb
%{_bindir}/filter_psms.rb
%{gem_extdir_mri}
%{gem_instdir}/bin
%{gem_libdir}
%exclude %{gem_cache}
%{gem_spec}

%files doc
%doc %{gem_docdir}
%doc %{gem_instdir}/README.md

%changelog
* Tue Sep 14 2021 mockbuilder - 1.4.4-1
- Initial package