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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)
import glob
import os
from spack import *
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-cgi', type='run')
depends_on('perl-dbd-sqlite', type='run')
def patch(self):
with working_dir(join_path(self.stage.source_path, 'admin/util')):
perlscripts = glob.glob('*.pl')
filter_file('#!/usr/bin/perl', '#!/usr/bin/env perl', *perlscripts)
# trinotate web generates a config on run but puts it in a bad place
# this causes issues with permissions; we hack the source to keep it
# in the calling user's homedir
filter_file('"$FindBin::RealBin/TrinotateWeb.conf/lighttpd.conf.port',
'$ENV{"HOME"} . "/.trinotate_lighttpd.conf.port',
'run_TrinotateWebserver.pl', string=True)
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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