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# Copyright 2013-2023 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 spack.package import *
class SnapKorf(MakefilePackage):
"""SNAP is a general purpose gene finding program suitable for both
eukaryotic and prokaryotic genomes."""
homepage = "http://korflab.ucdavis.edu/software.html"
url = "http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz"
git = "https://github.com/KorfLab/SNAP.git"
license("MIT")
version("2021-11-04", commit="62ff3120fceccb03b5eea9d21afec3167dedfa94")
version(
"2013-11-29", sha256="e2a236392d718376356fa743aa49a987aeacd660c6979cee67121e23aeffc66a"
)
depends_on("perl", type=("build", "run"))
def edit(self, spec, prefix):
if spec.satisfies("@2013-11-29%gcc@6:"):
rstr = "\\1 -Wno-tautological-compare -Wno-misleading-indentation"
filter_file("(-Werror)", rstr, "Zoe/Makefile")
rstr = "\\1 -Wno-error=format-overflow -Wno-misleading-indentation"
filter_file("(-Werror)", rstr, "Makefile")
filter_file(r"(^const char \* zoeFunction;)", "extern \\1", "Zoe/zoeTools.h")
filter_file(r"(^const char \* zoeConstructor;)", "extern \\1", "Zoe/zoeTools.h")
filter_file(r"(^const char \* zoeMethod;)", "extern \\1", "Zoe/zoeTools.h")
def install(self, spec, prefix):
mkdirp(prefix.bin)
progs = ["snap", "fathom", "forge"]
if spec.satisfies("@2013-11-29"):
progs = progs + ["depend", "exonpairs", "hmm-info"]
for p in progs:
install(p, prefix.bin)
install("*.pl", prefix.bin)
install_tree("Zoe", prefix.Zoe)
install_tree("HMM", prefix.HMM)
install_tree("DNA", prefix.DNA)
def setup_run_environment(self, env):
env.set("ZOE", self.prefix)
env.prepend_path("PATH", self.prefix)
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