text: # 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 *
  from glob import glob
  
  
  class Bowtie2(Package):
      """Bowtie 2 is an ultrafast and memory-efficient tool for aligning
         sequencing reads to long reference sequences"""
  
      homepage = "bowtie-bio.sourceforge.net/bowtie2/index.shtml"
      url      = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.3.1/bowtie2-2.3.1-source.zip"
  
      version('2.3.5.1', sha256='335c8dafb1487a4a9228ef922fbce4fffba3ce8bc211e2d7085aac092155a53f')
      version('2.3.5', sha256='2b6b2c46fbb5565ba6206b47d07ece8754b295714522149d92acebefef08347b')
      version('2.3.4.1', sha256='a1efef603b91ecc11cfdb822087ae00ecf2dd922e03c85eea1ed7f8230c119dc')
      version('2.3.1', sha256='33bd54f5041a31878e7e450cdcf0afba08345fa1133ce8ac6fd00bf7e521a443')
      version('2.3.0', sha256='f9f841e780e78b1ae24b17981e2469e6d5add90ec22ef563af23ae2dd5ca003c')
      version('2.2.5', sha256='e22766dd9421c10e82a3e207ee1f0eb924c025b909ad5fffa36633cd7978d3b0')
  
      depends_on('tbb', when='@2.3.0:')
      depends_on('readline', when='@2.3.1:')
      depends_on('perl', type='run')
      depends_on('python', type='run')
      depends_on('zlib', when='@2.3.1:')
  
      patch('bowtie2-2.2.5.patch', when='@2.2.5', level=0)
      patch('bowtie2-2.3.1.patch', when='@2.3.1', level=0)
      patch('bowtie2-2.3.0.patch', when='@2.3.0', level=0)
      resource(name='simde', git="https://github.com/nemequ/simde",
               destination='.', when='target=aarch64:')
  
      # seems to have trouble with 6's -std=gnu++14
      conflicts('%gcc@6:', when='@:2.3.1')
      conflicts('@:2.3.5.0', when='target=aarch64:')
  
      def patch(self):
          if self.spec.target.family == 'aarch64':
              copy_tree('simde', 'third_party/simde')
              if self.spec.satisfies('%gcc@:4.8.9'):
                  filter_file('-fopenmp-simd', '', 'Makefile')
  
      @run_before('install')
      def filter_sbang(self):
          """Run before install so that the standard Spack sbang install hook
             can fix up the path to the perl|python binary.
          """
  
          with working_dir(self.stage.source_path):
              kwargs = {'ignore_absent': True, 'backup': False, 'string': False}
  
              match = '^#!/usr/bin/env perl'
              perl = self.spec['perl'].command
              substitute = "#!{perl}".format(perl=perl)
              files = ['bowtie2', ]
              filter_file(match, substitute, *files, **kwargs)
  
              match = '^#!/usr/bin/env python'
              python = self.spec['python'].command
              substitute = "#!{python}".format(python=python)
              files = ['bowtie2-build', 'bowtie2-inspect']
              filter_file(match, substitute, *files, **kwargs)
  
      def install(self, spec, prefix):
          make_arg = []
          if self.spec.target.family == 'aarch64':
              make_arg.append('POPCNT_CAPABILITY=0')
          make(*make_arg)
          mkdirp(prefix.bin)
          for bow in glob("bowtie2*"):
              install(bow, prefix.bin)
          # install('bowtie2',prefix.bin)
          # install('bowtie2-align-l',prefix.bin)
          # install('bowtie2-align-s',prefix.bin)
          # install('bowtie2-build',prefix.bin)
          # install('bowtie2-build-l',prefix.bin)
          # install('bowtie2-build-s',prefix.bin)
          # install('bowtie2-inspect',prefix.bin)
          # install('bowtie2-inspect-l',prefix.bin)
          # install('bowtie2-inspect-s',prefix.bin)
  