text: # 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 Bsseeker2(Package):
      """A versatile aligning pipeline for bisulfite sequencing data."""
  
      homepage = "http://pellegrini.mcdb.ucla.edu/BS_Seeker2"
      url      = "https://github.com/BSSeeker/BSseeker2/archive/BSseeker2-v2.1.8.tar.gz"
  
      version('2.1.8', sha256='34ebedce36a0fca9e22405d4c2c20bc978439d4a34d1d543657fbc53ff847934')
      version('2.1.7', sha256='ac90fb4ad8853ee920f1ffea2b1a8cfffcdb1508ff34be0091d5a9c90ac8c74a',
              url='https://github.com/BSSeeker/BSseeker2/archive/v2.1.7.tar.gz')
      version('2.1.2', sha256='08055dd314f85a9b74c259c2cb894ea2affdab2c7a120af3589c649e1900c5c6',
              url='https://github.com/BSSeeker/BSseeker2/archive/v2.1.2.tar.gz')
  
      depends_on('python@2.6:', type=('build', 'run'))
      depends_on('py-pysam', type=('build', 'run'))
  
      def install(self, spec, prefix):
          mkdirp(prefix.bin)
          install('Antisense.py', prefix.bin)
          install_tree('bs_index', prefix.bin.bs_index)
          install('bs_seeker2-build.py', prefix.bin)
          install_tree('bs_utils', prefix.bin.bs_utils)
          install_tree('galaxy', prefix.bin.galaxy)
          install_tree('bs_align', prefix.bin.bs_align)
          install('bs_seeker2-align.py', prefix.bin)
          install('bs_seeker2-call_methylation.py', prefix.bin)
          install('FilterReads.py', prefix.bin)
  