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 Kallisto(CMakePackage):
      """kallisto is a program for quantifying abundances of transcripts from
         RNA-Seq data."""
  
      homepage = "http://pachterlab.github.io/kallisto"
      url      = "https://github.com/pachterlab/kallisto/archive/v0.43.1.tar.gz"
  
      version('0.46.2', sha256='c447ca8ddc40fcbd7d877d7c868bc8b72807aa8823a8a8d659e19bdd515baaf2')
      version('0.43.1', sha256='7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400')
  
      depends_on('zlib')
      depends_on('hdf5')
      depends_on('mpich')
  
      # htslib isn't built in time to be used....
      parallel = False
  
      # v0.44.0 vendored a copy of htslib and uses auto* to build
      # its configure script.
      depends_on('autoconf', type='build', when='@0.44.0:')
      depends_on('automake', type='build', when='@0.44.0:')
      depends_on('libtool',  type='build', when='@0.44.0:')
      depends_on('m4',       type='build', when='@0.44.0:')
  
      # Including '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' in the cmake args
      # causes bits of cmake's output to end up in the autoconf-generated
      # configure script.
      # See https://github.com/spack/spack/issues/15274 and
      # https://github.com/pachterlab/kallisto/issues/253
      @property
      def std_cmake_args(self):
          """Call the original std_cmake_args and then filter the verbose
          setting.
          """
          a = super(Kallisto, self).std_cmake_args
          if (self.spec.version >= Version('0.44.0')):
              args = [i for i in a if i != '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON']
          else:
              args = a
  
          return args
  
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 Kallisto(CMakePackage):
      """kallisto is a program for quantifying abundances of transcripts from
         RNA-Seq data."""
  
      homepage = "http://pachterlab.github.io/kallisto"
      url      = "https://github.com/pachterlab/kallisto/archive/v0.43.1.tar.gz"
  
      version('0.46.2', sha256='c447ca8ddc40fcbd7d877d7c868bc8b72807aa8823a8a8d659e19bdd515baaf2')
      version('0.43.1', sha256='7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400')
  
      depends_on('zlib')
      depends_on('hdf5')
  
      # htslib isn't built in time to be used....
      parallel = False
  
      # v0.44.0 vendored a copy of htslib and uses auto* to build
      # its configure script.
      depends_on('autoconf', type='build', when='@0.44.0:')
      depends_on('automake', type='build', when='@0.44.0:')
      depends_on('libtool',  type='build', when='@0.44.0:')
      depends_on('m4',       type='build', when='@0.44.0:')
  
      # Including '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' in the cmake args
      # causes bits of cmake's output to end up in the autoconf-generated
      # configure script.
      # See https://github.com/spack/spack/issues/15274 and
      # https://github.com/pachterlab/kallisto/issues/253
      @property
      def std_cmake_args(self):
          """Call the original std_cmake_args and then filter the verbose
          setting.
          """
          a = super(Kallisto, self).std_cmake_args
          if (self.spec.version >= Version('0.44.0')):
              args = [i for i in a if i != '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON']
          else:
              args = a
  
          return args
  
subject: remove mpich dependency (#17551)