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File primer3.spec of Package primer3

#
# spec file for package primer3
#
# Copyright (c) 2013 SUSE LINUX Products GmbH, Nuernberg, Germany.
#
# 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 http://bugs.opensuse.org/
#

%define p3home %{_datadir}/primer3

Name:           primer3
Summary:        Command line tool to select primers for polymerase chain reaction (PCR)
License:        GPL-2.0 and GPL-3.0
# Amplicon3 is GPL3
Group:          Productivity/Scientific/Other
Version:        2.6.1
Release:        0
Source:         https://github.com/primer3-org/primer3/archive/refs/tags/v%{version}.tar.gz
Url:            https://primer3.org/
BuildRequires:  gcc-c++
BuildRoot:      %{_tmppath}/%{name}-%{version}-build

%description
Primer3 is a widely used program for designing PCR primers (PCR = "Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.

PCR is used for many different goals. Consequently, primer3 has many different input parameters that you control and that tell primer3 exactly what characteristics make good primers for your goals.

%package docs
Summary:        Documentation for %{name}
Group:          Documentation/Other

%description docs
The %{name}-docs package includes the documentation for %{name}.

%package test
Summary:        Test files for %{name}
Group:          Productivity/Scientific/Other
Requires:       %{name} = %{version}-%{release}

%description test
The %{name}-test package includes the test files for %{name}. Run 'make test' in the folder '/usr/share/primer3/test' to perform the tests.

%prep
%setup -q

%build
cd ./src

make all RPM_OPT_FLAGS="%{optflags}"

%install
rm -rf %{buildroot}

mkdir -p %{buildroot}%{_bindir}
install -sm 755 ./src/amplicon3_core %{buildroot}%{_bindir}/amplicon3_core
install -sm 755 ./src/long_seq_tm_test %{buildroot}%{_bindir}/long_seq_tm_test
install -sm 755 ./src/ntdpal %{buildroot}%{_bindir}/ntdpal
install -sm 755 ./src/ntthal %{buildroot}%{_bindir}/ntthal
install -sm 755 ./src/oligotm %{buildroot}%{_bindir}/oligotm
install -sm 755 ./src/primer3_core %{buildroot}%{_bindir}/primer3_core
install -sm 755 ./src/primer3_masker %{buildroot}%{_bindir}/primer3_masker

#create symlink to use version 2 of primer3 with EMBOSS
ln -s ./primer3_core %{buildroot}%{_bindir}/primer32_core

#move primer3_config to /usr/share/primer3
mkdir -p %{buildroot}%{p3home}/primer3_config/interpretations
install -m 644 ./src/primer3_config/interpretations/* %{buildroot}%{p3home}/primer3_config/interpretations/
rm -rf ./src/primer3_config/interpretations
install -m 644 ./src/primer3_config/* %{buildroot}%{p3home}/primer3_config/

#move settings_files to /usr/share/primer3
mkdir -p %{buildroot}%{p3home}/settings_files
install -m 644 ./settings_files/* %{buildroot}%{p3home}/settings_files/

#move doc to /usr/share/doc/packages/primer3
mkdir -p %{buildroot}%{_datadir}/doc/packages/primer3
install -m 644 ./src/release_notes.txt ./src/primer3_manual.htm ./src/LICENSE_GPL3_for_Amplicon3 ./src/LICENSE ./example %{buildroot}%{_datadir}/doc/packages/primer3/

#two test scripts have /usr/local/bin/perl as shebang
sed -i 's/\/usr\/local\/bin\/perl/\/usr\/bin\/perl/' ./test/long_seq_tm_test.pl
sed -i 's/\/usr\/local\/bin\/perl/\/usr\/bin\/perl/' ./test/vgrep.pl

#there is no need to first build the binaries when the test script is executed
sed -i 's/cd ..\/src; make/# cd ..\/src; make/' ./test/Makefile

#move test files to /usr/share/primer3
mkdir -p %{buildroot}%{p3home}/kmer_lists
install -m 644 ./kmer_lists/* %{buildroot}%{p3home}/kmer_lists/
mkdir -p %{buildroot}%{p3home}/test
install -m 755 ./test/Makefile %{buildroot}%{p3home}/test/
rm ./test/Makefile
install -m 755 ./test/*.pl %{buildroot}%{p3home}/test/
rm ./test/*.pl
install -m 755 ./test/*.r %{buildroot}%{p3home}/test/
rm ./test/*.r
find ./test -type f -exec install -Dm 644 "{}" "%{buildroot}%{p3home}/{}" \;

#create links to the binary files in /usr/share/primer3/src, as the test scripts in /usr/share/primer3/test require the binaries and the file humrep_and_simple.txt in ../src
mkdir -p %{buildroot}%{p3home}/src
ln -s /usr/bin/amplicon3_core %{buildroot}%{p3home}/src/amplicon3_core
ln -s /usr/bin/long_seq_tm_test %{buildroot}%{p3home}/src/long_seq_tm_test
ln -s /usr/bin/ntdpal %{buildroot}%{p3home}/src/ntdpal
ln -s /usr/bin/ntthal %{buildroot}%{p3home}/src/ntthal
ln -s /usr/bin/oligotm %{buildroot}%{p3home}/src/oligotm
ln -s /usr/bin/primer3_core %{buildroot}%{p3home}/src/primer3_core
ln -s /usr/bin/primer3_masker %{buildroot}%{p3home}/src/primer3_masker
install -m 644 ./src/humrep_and_simple.txt %{buildroot}%{p3home}/src/

%clean

%files
%defattr(-,root,root,-)
%{_bindir}/*
%{p3home}
%{p3home}/primer3_config
%{p3home}/settings_files
%exclude %{p3home}/test
%exclude %{p3home}/kmer_lists
%exclude %{p3home}/src

%files docs
%defattr(-,root,root,-)
%{_datadir}/doc/packages/primer3

%files test
%defattr(-,root,root,-)
%{p3home}/test
%{p3home}/kmer_lists
%{p3home}/src

%changelog
* Sun Aug 07 2022 Tobias Schwarz <mail@tobias-schwarz.net> - 2.6.1
- Update to version 2.6.1
- Added docs package
- Added test package

* Thu Jun 01 2017 Tobias Schwarz <mail@tobias-schwarz.net> - 2.3.7
- Update to version 2.3.7

* Thu May 30 2013 Tobias Schwarz <mail@tobias-schwarz.net> - 2.3.5
- First release

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File primer3.spec of Package primer3

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