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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 Eagle(MakefilePackage):
"""EAGLE: Explicit Alternative Genome Likelihood Evaluator"""
homepage = "https://github.com/tony-kuo/eagle"
url = "https://github.com/tony-kuo/eagle/archive/v1.1.2.tar.gz"
maintainers("snehring")
license("GPL-3.0-only")
version("1.1.3", sha256="bd510b8eef2de14898cbf417e1c7a30b97ddaba24e5e2834da7b02767362fe3c")
version("1.1.2", sha256="afe967560d1f8fdbd0caf4b93b5f2a86830e9e4d399fee4a526140431343045e")
depends_on("curl")
depends_on("zlib-api")
depends_on("lzma")
depends_on("htslib")
def edit(self, spec, prefix):
# remove unused gcc flags
filter_file("$(LFLAGS) $(INCLUDES)", "", "Makefile", string=True)
# drop static link to htslib
filter_file("$(LIBS)", "", "Makefile", string=True)
# don't try to build htslib.
filter_file("all: UTIL HTSLIB", "all: UTIL", "Makefile", string=True)
# add htslib link to ldflags
filter_file("-lcurl", "-lcurl -lhts", "Makefile", string=True)
# use spack C compiler
filter_file("CC=.*", "CC={0}".format(spack_cc), "Makefile")
# let the user inject march if they want
filter_file("-march=native", "", "Makefile", string=True)
def install(self, spec, prefix):
mkdirp(prefix.bin)
bins = ["eagle", "eagle-rc", "eagle-nm"]
for b in bins:
install(b, prefix.bin)
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