%global         debug_package   %{nil}
%global         java_version    1.8.0

Name:           trimmomatic
Version:        0.39
Release:        1
Summary:        Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.

License:        GPL-3.0-only
URL:            https://github.com/usadellab/Trimmomatic
Source0:        %{url}/archive/refs/tags/v%{version}.tar.gz#/Trimmomatic-%{version}.tar.gz

BuildRequires:  ant java-%{java_version}-devel
Requires:       javapackages-tools

%description
Trimmomatic performs a variety of useful trimming tasks for illumina paired-end
and single ended data.The current trimming steps are:
 ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the read.
 SLIDINGWINDOW: Perform a sliding window trimming, cutting once the average quality 
within the window falls below a threshold.
 LEADING: Cut bases off the start of a read, if below a threshold quality
 TRAILING: Cut bases off the end of a read, if below a threshold quality
 CROP: Cut the read to a specified length
 HEADCROP: Cut the specified number of bases from the start of the read
 MINLEN: Drop the read if it is below a specified length
 TOPHRED33: Convert quality scores to Phred-33
 TOPHRED64: Convert quality scores to Phred-64

%prep
%autosetup -n Trimmomatic-%{version}

%build
%ant

%install
install -d -p -m 0755 %{buildroot}%{_javadir}
install -D -p -m 0644 ./dist/jar/%{name}-%{version}.jar %{buildroot}%{_javadir}/%{name}-%{version}.jar

pushd %{buildroot}%{_javadir} || exit 1
ln -sf %{name}-%{version}.jar %{name}.jar
popd

install -d -p -m 0755 %{buildroot}%{_datadir}/%{name}
install -D -p -m 0644 ./adapters/* %{buildroot}%{_datadir}/%{name}

%files
%doc README.md
%license ./distSrc/LICENSE
%{_javadir}/%{name}-%{version}.jar
%{_javadir}/%{name}.jar
%{_datadir}/%{name}/*

%changelog
* Wed Jun 23 2021 yang kang <[email protected]> - 0.39-1
- Package init