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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 os import symlink
from spack.package import *
class Recon(MakefilePackage):
"""RECON: a package for automated de novo identification of repeat families
from genomic sequences."""
homepage = "http://eddylab.org/software/recon/"
url = "http://eddylab.org/software/recon/RECON1.05.tar.gz"
version('1.05', sha256='4d4f76f439bcffd50380cffc41a80dc15fa4a80f38a04234e24da893ed7c025a')
variant('repeatmasker', default=False,
description='Use RepeatMasker developer patches (1.08)')
patch('repeatmasker_recon.patch', when='+repeatmasker')
build_directory = 'src'
depends_on('perl', type='run')
@property
def install_targets(self):
return [
'install',
'BINDIR=%s' % self.prefix.bin
]
# edit the recon.pl script with the prefix as mentioned in the README
def edit(self, spec, prefix):
filter_file('$path = ""', '$path = "%s"' % prefix.bin,
'scripts/recon.pl', string=True)
# recon's makefile is very basic -- the target directory must
# already exist to properly install
@run_before('install')
def prepare_bin(self):
mkdirp(prefix.bin)
# finally, install the scripts dir as well
# and link the recon command into bin.
@run_after('install')
def finalize(self):
install_tree('scripts', prefix.scripts)
symlink(join_path(prefix.scripts, 'recon.pl'),
join_path(prefix.bin, 'recon'))
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