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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 os import symlink
from spack.package import *
class Fasttree(Package):
"""FastTree infers approximately-maximum-likelihood phylogenetic
trees from alignments of nucleotide or protein sequences.
"""
homepage = "http://www.microbesonline.org/fasttree"
url = "http://www.microbesonline.org/fasttree/FastTree-2.1.10.c"
maintainers("snehring")
version(
"2.1.11",
sha256="9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f",
expand=False,
url="http://www.microbesonline.org/fasttree/FastTree-2.1.11.c",
)
version(
"2.1.10",
sha256="54cb89fc1728a974a59eae7a7ee6309cdd3cddda9a4c55b700a71219fc6e926d",
expand=False,
url="http://www.microbesonline.org/fasttree/FastTree-2.1.10.c",
)
variant("openmp", default=True, description="Add openmp support to Fasttree.")
def install(self, spec, prefix):
cc = Executable(spack_cc)
if "+openmp" in self.spec:
cc(
"-O3",
self.compiler.openmp_flag,
"-DOPENMP",
"-finline-functions",
"-funroll-loops",
"-Wall",
"-oFastTree",
"FastTree-" + format(spec.version.dotted) + ".c",
"-lm",
)
else:
cc(
"-O3",
"-finline-functions",
"-funroll-loops",
"-Wall",
"-oFastTree",
"FastTree-" + format(spec.version.dotted) + ".c",
"-lm",
)
mkdir(prefix.bin)
install("FastTree", prefix.bin)
@run_after("install")
def create_fasttree_mp_symlink(self):
with working_dir(prefix.bin):
if "+openmp" in self.spec:
symlink("FastTree", "FastTreeMP")
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