48 lines
1.7 KiB
Python
48 lines
1.7 KiB
Python
# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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import glob
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from spack.package import *
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class Guidance(MakefilePackage):
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"""Guidance: Accurate detection of unreliable alignment regions accounting
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for the uncertainty of multiple parameters."""
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homepage = "http://guidance.tau.ac.il/ver2/"
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url = "http://guidance.tau.ac.il/ver2/guidance.v2.02.tar.gz"
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version("2.02", sha256="825e105dde526759fb5bda1cd539b24db0b90b8b586f26b1df74d9c5abaa7844")
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depends_on("perl", type=("build", "run"))
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depends_on("perl-bioperl", type=("build", "run"))
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depends_on("ruby")
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depends_on("prank")
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depends_on("clustalw")
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depends_on("mafft")
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depends_on("muscle")
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conflicts("%gcc@6.2.0:")
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def edit(self, spec, prefix):
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for dir in "Guidance", "Selecton", "bioSequence_scripts_and_constants":
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with working_dir(join_path("www", dir)):
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files = glob.iglob("*.pl")
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for file in files:
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perl = FileFilter(file)
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perl.filter("#!/usr/bin/perl -w", "#!/usr/bin/env perl")
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def install(self, spac, prefix):
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mkdir(prefix.bin)
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install_tree("libs", prefix.bin.libs)
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install_tree("programs", prefix.bin.programs)
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install_tree("www", prefix.bin.www)
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with working_dir(join_path("www", "Guidance")): # copy without suffix
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install("guidance.pl", join_path(prefix.bin.www.Guidance, "guidance"))
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def setup_run_environment(self, env):
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env.prepend_path("PATH", prefix.bin.www.Guidance)
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