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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 Hapcut2(MakefilePackage):
"""HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes
from DNA sequence reads, designed to 'just work' with excellent speed
and accuracy."""
homepage = "https://github.com/vibansal/HapCUT2"
git = "https://github.com/vibansal/HapCUT2.git"
maintainers("snehring")
license("BSD-2-Clause")
version("v1.3.1", commit="c6481d5fd0618dc3e82b2eb8c2b4835d9a4f6da7")
version(
"2017-07-10",
commit="2966b94c2c2f97813b757d4999b7a6471df1160e",
submodules=True,
deprecated=True,
)
depends_on("htslib@1.3:")
depends_on("curl")
depends_on("openssl")
depends_on("xz")
depends_on("bzip2")
depends_on("zlib-api")
@when("@v1.3.1:")
def edit(self, spec, prefix):
filter_file("CC=.*$", "", "Makefile")
filter_file("CFLAGS=.*$", "CFLAGS=-Wall -g -O3 -D_GNU_SOURCE", "Makefile")
with working_dir("hairs-src"):
filter_file(r"(keyvalue\* keypointer;)", "extern \\1", "hashtable.h")
filter_file(r"(keypointer = ht->blist\[hash\];)", "keyvalue* \\1", "hashtable.c")
def install(self, spec, prefix):
mkdirp(prefix.bin)
with working_dir("build"):
if self.spec.satisfies("@2017-07-10"):
install("extractFOSMID", prefix.bin)
install("extractHAIRS", prefix.bin)
install("HAPCUT2", prefix.bin)
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