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# Copyright 2013-2024 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"
license("GPL-2.0-only")
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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