# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)

import os
from spack import *


class Rnaquast(Package):
    """Quality assessment of de novo transcriptome assemblies from RNA-Seq data

    rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome
    and gene database. In addition, rnaQUAST is also capable of estimating gene
    database coverage by raw reads and de novo quality assessment
    using third-party software."""

    homepage = "https://github.com/ablab/rnaquast"
    url      = "https://github.com/ablab/rnaquast/archive/refs/tags/v2.2.0.tar.gz"

    maintainers = ['dorton21']

    version('2.2.0', sha256='117dff9d9c382ba74b7b0ff24bc7b95b9ca6aa701ebf8afd22943aa54e382334')

    depends_on('python@2.5:', type=('build', 'run'))
    depends_on('py-matplotlib', type=('build', 'run'))
    depends_on('py-joblib', type=('build', 'run'))
    depends_on('py-gffutils', type=('build', 'run'))
    depends_on('gmap-gsnap', type=('build', 'run'))
    depends_on('blast-plus', type=('build', 'run'))

    def install(self, spec, prefix):
        install_tree('.', prefix.bin)
        os.rename('%s/rnaQUAST.py' % prefix.bin, '%s/rnaQUAST' % prefix.bin)

    def setup_run_environment(self, env):
        env.prepend_path('PATH', prefix.bin)

add new package (#22648)