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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 spack.package import *
class Nseg(MakefilePackage):
"""NSEG - Low complexity sequence identification"""
homepage = "ftp://ftp.ncbi.nih.gov/pub/seg/nseg/"
url = "ftp://ftp.ncbi.nih.gov/pub/seg/nseg/nseg.c"
version(
"1.0",
sha256="afae364fbe51caa1eccb704ed0b954437a3ef48a0cd3bf473f4b61d6fde9617e",
expand=False,
)
resource(
name="makefile",
url="ftp://ftp.ncbi.nih.gov/pub/seg/nseg/makefile",
sha256="32937aef6969550ca3c762b5dd61b1520635cc46e773e35e56c5718f75838cee",
expand=False,
)
resource(
name="genwin.c",
url="ftp://ftp.ncbi.nih.gov/pub/seg/nseg/genwin.c",
sha256="d392d2db625dc8c90b00f2a86028a3a45d121e15eb403b51c2f9b01692ab10d9",
expand=False,
)
resource(
name="genwin.h",
url="ftp://ftp.ncbi.nih.gov/pub/seg/nseg/genwin.h",
sha256="1c701d87bf6200bfa40faa16fe665828a010727ef1aa0e8a1e5823605165fb86",
expand=False,
)
resource(
name="lnfac.h",
url="ftp://ftp.ncbi.nih.gov/pub/seg/nseg/lnfac.h",
sha256="5048e4f3dc3a7ea420d4eb4912a661f285634fbb205411b647b1f00c3fe3a0d2",
expand=False,
)
resource(
name="nmerge.c",
url="ftp://ftp.ncbi.nih.gov/pub/seg/nseg/nmerge.c",
sha256="c8a4bb4c960acf7fcd7509b635766b618efdab9f09aec36443040759eca3bce3",
expand=False,
)
resource(
name="runnseg",
url="ftp://ftp.ncbi.nih.gov/pub/seg/nseg/runnseg",
sha256="2830a5a1c5ea1a879cf3a415dfbb23db7a81e84d41698ddf765f2e1ef42e7c78",
expand=False,
)
build_directory = "nseg"
@run_before("build")
def prepare_source(self):
# create the build dir
mkdirp(self.build_directory)
# move the primary source file in
copy("nseg.c", join_path(self.build_directory, "nseg.c"))
# move all of the single-file resources into the build dir
for key in self.resources:
for res in self.resources[key]:
res_name = res.name
res_path = join_path(res.fetcher.stage.source_path, res.name)
copy(res_path, join_path(self.build_directory, res_name))
if self.spec.satisfies("%fj"):
sfiles = ["genwin.c", "nseg.c"]
for s_name in sfiles:
filter_file(
"return;", "return 0;", join_path(self.build_directory, s_name), string=True
)
def install(self, spec, prefix):
with working_dir(self.build_directory):
mkdirp(prefix.bin)
install("nseg", prefix.bin)
install("nmerge", prefix.bin)
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