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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)
import glob
from spack.package import *
class Guidance(MakefilePackage):
"""Guidance: Accurate detection of unreliable alignment regions accounting
for the uncertainty of multiple parameters."""
homepage = "http://guidance.tau.ac.il/ver2/"
url = "http://guidance.tau.ac.il/ver2/guidance.v2.02.tar.gz"
version("2.02", sha256="825e105dde526759fb5bda1cd539b24db0b90b8b586f26b1df74d9c5abaa7844")
depends_on("perl", type=("build", "run"))
depends_on("perl-bioperl", type=("build", "run"))
depends_on("ruby")
depends_on("prank")
depends_on("clustalw")
depends_on("mafft")
depends_on("muscle")
conflicts("%gcc@6.2.0:")
def edit(self, spec, prefix):
for dir in "Guidance", "Selecton", "bioSequence_scripts_and_constants":
with working_dir(join_path("www", dir)):
files = glob.iglob("*.pl")
for file in files:
perl = FileFilter(file)
perl.filter("#!/usr/bin/perl -w", "#!/usr/bin/env perl")
def install(self, spac, prefix):
mkdir(prefix.bin)
install_tree("libs", prefix.bin.libs)
install_tree("programs", prefix.bin.programs)
install_tree("www", prefix.bin.www)
with working_dir(join_path("www", "Guidance")): # copy without suffix
install("guidance.pl", join_path(prefix.bin.www.Guidance, "guidance"))
def setup_run_environment(self, env):
env.prepend_path("PATH", prefix.bin.www.Guidance)
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