old_contents: # Copyright 2013-2020 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)
  
      def install(self, spec, prefix):
          mkdirp(prefix.bin)
  
          bins = [
              'eagle',
              'eagle-rc',
              'eagle-nm',
          ]
  
          for b in bins:
              install(b, prefix.bin)
  
new_contents: # Copyright 2013-2020 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)
  
subject: fix CC=gcc and delete march=native (#17763)