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# 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)
from spack import *
from os import symlink
class LtrRetriever(Package):
"""LTR_retriever is a highly accurate and sensitive program for
identification of LTR retrotransposons."""
homepage = "https://github.com/oushujun/LTR_retriever"
url = "https://github.com/oushujun/LTR_retriever/archive/v2.8.7.tar.gz"
version('2.8.7', sha256='29ca6f699c57b5e964aa0ee6c7d3e1e4cd5362dadd789e5f0e8c82fe0bb29369')
depends_on('perl', type='run')
depends_on('blast-plus', type='run')
depends_on('hmmer@3.1b2:', type='run')
depends_on('cdhit', type='run')
depends_on('repeatmasker', type='run')
def install(self, spec, prefix):
filter_file(r'BLAST\+=.*', 'BLAST+=%s' % spec['blast-plus'].prefix.bin,
'paths')
filter_file('RepeatMasker=.*',
'RepeatMasker=%s' % spec['repeatmasker'].prefix.bin,
'paths')
filter_file('HMMER=.*',
'HMMER=%s' % spec['hmmer'].prefix.bin,
'paths')
filter_file('CDHIT=.*',
'CDHIT=%s' % spec['cdhit'].prefix,
'paths')
filter_file('BLAST=.*', '', 'paths')
mkdirp(prefix.opt)
mkdirp(prefix.bin)
install_tree('.', prefix.opt.ltr_retriever)
symlink(prefix.opt.ltr_retriever.LTR_retriever,
prefix.bin.LTR_retriever)
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