old_contents: ##############################################################################
  # Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
  # Produced at the Lawrence Livermore National Laboratory.
  #
  # This file is part of Spack.
  # Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
  # LLNL-CODE-647188
  #
  # For details, see https://github.com/spack/spack
  # Please also see the NOTICE and LICENSE files for our notice and the LGPL.
  #
  # This program is free software; you can redistribute it and/or modify
  # it under the terms of the GNU Lesser General Public License (as
  # published by the Free Software Foundation) version 2.1, February 1999.
  #
  # This program is distributed in the hope that it will be useful, but
  # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
  # conditions of the GNU Lesser General Public License for more details.
  #
  # You should have received a copy of the GNU Lesser General Public
  # License along with this program; if not, write to the Free Software
  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
  ##############################################################################
  from spack import *
  
  
  class PyPysam(PythonPackage):
      """A python module for reading, manipulating and writing genomic data
         sets."""
  
      homepage = "https://pypi.python.org/pypi/pysam"
      url      = "https://pypi.io/packages/source/p/pysam/pysam-0.11.2.2.tar.gz"
  
      version('0.13', 'a9b502dd1a7e6403e35e6972211688a2')
      version('0.11.2.2', '56230cd5f55b503845915b76c22d620a')
      version('0.7.7', 'eaf9f37cbccc5e2708754d045909c1a0')
  
      depends_on('py-setuptools', type='build')
      depends_on('py-cython@0.21:', type='build')
      depends_on('bcftools')
  
new_contents: ##############################################################################
  # Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
  # Produced at the Lawrence Livermore National Laboratory.
  #
  # This file is part of Spack.
  # Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
  # LLNL-CODE-647188
  #
  # For details, see https://github.com/spack/spack
  # Please also see the NOTICE and LICENSE files for our notice and the LGPL.
  #
  # This program is free software; you can redistribute it and/or modify
  # it under the terms of the GNU Lesser General Public License (as
  # published by the Free Software Foundation) version 2.1, February 1999.
  #
  # This program is distributed in the hope that it will be useful, but
  # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
  # conditions of the GNU Lesser General Public License for more details.
  #
  # You should have received a copy of the GNU Lesser General Public
  # License along with this program; if not, write to the Free Software
  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
  ##############################################################################
  from spack import *
  
  
  class PyPysam(PythonPackage):
      """A python module for reading, manipulating and writing genomic data
         sets."""
  
      homepage = "https://pypi.python.org/pypi/pysam"
      url      = "https://github.com/pysam-developers/pysam/archive/v0.14.1.tar.gz"
  
      version('0.14.1', 'ad88fa5bbcc0fdf4a936734691d9c9d1')
      version('0.13', 'a9b502dd1a7e6403e35e6972211688a2')
      version('0.11.2.2', '56230cd5f55b503845915b76c22d620a')
      version('0.7.7', 'eaf9f37cbccc5e2708754d045909c1a0')
  
      depends_on('py-setuptools', type='build')
      depends_on('py-cython@0.21:', type='build')
      depends_on('curl')
      depends_on('bcftools')
      depends_on('htslib')
      depends_on('samtools')
  
      depends_on('htslib@:1.6', when='@:0.13')
  
subject: Bump pysam to 0.14.1. (#7988)