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# 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)
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