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# Copyright 2013-2018 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 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 = "http://transdecoder.github.io/"
url = "https://github.com/TransDecoder/TransDecoder/archive/v3.0.1.tar.gz"
version('3.0.1', 'f62b86a15fcb78b1dada9f80cc25f300')
depends_on('perl', type=('build', 'run'))
depends_on('perl-uri-escape', type='run')
def install(self, spec, prefix):
mkdirp(prefix.bin)
install('TransDecoder.LongOrfs', prefix)
install('TransDecoder.Predict', prefix)
install_tree('PerlLib', prefix.PerlLib)
install_tree('util', prefix.util)
def setup_environment(self, spack_env, run_env):
run_env.prepend_path('PATH', prefix.util.bin)
run_env.prepend_path('PATH', prefix)
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