text: # Copyright 2013-2022 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.package import *
  
  
  class Shortbred(Package):
      """ShortBRED is a system for profiling protein families of interest at
      very high specificity in shotgun meta'omic sequencing data."""
  
      homepage = "https://huttenhower.sph.harvard.edu/shortbred"
      url      = "https://bitbucket.org/biobakery/shortbred/get/0.9.4.tar.gz"
  
      version('0.9.4', sha256='a85e5609db79696d3f2d478408fc6abfeea7628de9f533c4e1e0ea3622b397ba')
  
      depends_on('blast-plus@2.2.28:')
      depends_on('cdhit@4.6:')
      depends_on('muscle@3.8.31:')
      depends_on('python@2.7.9:')
      depends_on('py-biopython')
      depends_on('usearch@6.0.307:')
  
      def install(self, spec, prefix):
          mkdirp(prefix.bin)
          install('shortbred_identify.py', prefix.bin)
          install('shortbred_quantify.py', prefix.bin)
          install_tree('src', prefix.src)
  
      def setup_run_environment(self, env):
          env.prepend_path('PYTHONPATH', self.prefix)
  