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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 *
import os
class Trinotate(Package):
"""Trinotate is a comprehensive annotation suite designed for
automatic functional annotation of transcriptomes, particularly
de novo assembled transcriptomes, from model or non-model organisms"""
homepage = "https://trinotate.github.io/"
url = "https://github.com/Trinotate/Trinotate/archive/Trinotate-v3.1.1.tar.gz"
version('3.1.1', sha256='f8af0fa5dbeaaf5a085132cd4ac4f4206b05cc4630f0a17a672c586691f03843')
depends_on('trinity', type='run')
depends_on('transdecoder', type='run')
depends_on('sqlite', type='run')
depends_on('ncbi-rmblastn', type='run')
depends_on('hmmer', type='run')
depends_on('perl', type='run')
depends_on('lighttpd', type='run')
depends_on('perl-dbi', type='run')
depends_on('perl-dbd-mysql', type='run')
depends_on('perl-cgi', type='run')
def install(self, spec, prefix):
# most of the perl modules have local deps, install the whole tree
mkdirp(prefix.lib)
install_tree('.', join_path(prefix.lib, 'trinotate'))
mkdirp(prefix.bin)
os.symlink(join_path(prefix.lib, 'trinotate/Trinotate'),
join_path(prefix.bin, 'Trinotate'))
os.symlink(join_path(prefix.lib,
'trinotate/run_TrinotateWebserver.pl'),
join_path(prefix.bin, 'run_TrinotateWebserver.pl'))
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