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# Copyright 2013-2021 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 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"
version('1.1.2', sha256='afe967560d1f8fdbd0caf4b93b5f2a86830e9e4d399fee4a526140431343045e')
depends_on('curl')
depends_on('zlib')
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')
# remove march=native %fj
if self.spec.satisfies('%fj'):
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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