# Copyright 2013-2022 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)

from spack.package import *


class Transdecoder(MakefilePackage):
    """TransDecoder identifies candidate coding regions within transcript
       sequences, such as those generated by de novo RNA-Seq transcript
       assembly using Trinity, or constructed based on RNA-Seq alignments to
       the genome using Tophat and Cufflinks."""

    homepage = "https://transdecoder.github.io/"
    url      = "https://github.com/TransDecoder/TransDecoder/archive/TransDecoder-v5.5.0.tar.gz"

    version('5.5.0', sha256='c800d9226350817471e9f51267c91f7cab99dbc9b26c980527fc1019e7d90a76')
    version('3.0.1', sha256='753a5fac5bfd04466aeabff48053c92e876cece8906b96de3b72f23f86fafae7',
            url='https://github.com/TransDecoder/TransDecoder/archive/v3.0.1.tar.gz')

    depends_on('perl', type=('build', 'run'))
    depends_on('perl-uri', type='run')

    def install(self, spec, prefix):
        mkdirp(prefix.util)
        install('TransDecoder.LongOrfs', prefix)
        install('TransDecoder.Predict', prefix)
        install_tree('PerlLib', prefix.PerlLib)
        install_tree('util', prefix.util)

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