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 *
  
  
  class Strelka(CMakePackage):
      """Somatic and germline small variant caller for mapped sequencing
         data."""
  
      homepage = "https://github.com/Illumina/strelka"
      url      = "https://github.com/Illumina/strelka/releases/download/v2.8.2/strelka-2.8.2.release_src.tar.bz2"
  
      version('2.8.2', sha256='27415f7c14f92e0a6b80416283a0707daed121b8a3854196872981d132f1496b')
  
      depends_on('python@2.4:')
      depends_on('zlib')
      depends_on('bzip2')
      depends_on('cmake@2.8.5:')
      depends_on('boost@1.56.0:')
  
      @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 python binary.
          """
  
          match = '^#!/usr/bin/env python'
          python = self.spec['python'].command
          substitute = "#!{p}".format(p=python)
          kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
          with working_dir('src'):
              files = [
                  'config/validate/validateJsonModelFromSchema.py',
                  'srcqc/run_cppcheck.py',
                  'python/libexec/cat.py',
                  'python/libexec/sortVcf.py',
                  'python/libexec/extractSmallIndelCandidates.py',
                  'python/libexec/configureStrelkaNoiseWorkflow.py',
                  'python/libexec/configureSequenceErrorCountsWorkflow.py',
                  'python/libexec/vcfCmdlineSwapper.py',
                  'python/libexec/mergeChromDepth.py',
                  'python/scoringModelTraining/germline/bin/evs_learn.py',
                  'python/scoringModelTraining/germline/bin/parseAnnotatedTrainingVcf.py',  # noqa: E501
                  'python/scoringModelTraining/germline/bin/filterTrainingVcf.py',  # noqa: E501
                  'python/scoringModelTraining/germline/bin/evs_exportmodel.py',
                  'python/scoringModelTraining/germline/bin/evs_qq.py',
                  'python/scoringModelTraining/germline/bin/evs_pr.py',
                  'python/scoringModelTraining/germline/bin/evs_evaluate.py',
                  'python/scoringModelTraining/somatic/bin/evs_random_sample_tpfp.py',  # noqa: E501
                  'python/scoringModelTraining/somatic/bin/evs_learn.py',
                  'python/scoringModelTraining/somatic/bin/evs_random_split_csv.py',  # noqa: E501
                  'python/scoringModelTraining/somatic/bin/vcf_to_feature_csv.py',  # noqa: E501
                  'python/scoringModelTraining/somatic/bin/calc_features.py',
                  'python/scoringModelTraining/somatic/bin/evs_exportmodel.py',
                  'python/scoringModelTraining/somatic/bin/evs_pr.py',
                  'python/scoringModelTraining/somatic/bin/evs_evaluate.py',
                  'python/bin/configureStrelkaGermlineWorkflow.py',
                  'python/bin/configureStrelkaSomaticWorkflow.py',
              ]
              filter_file(match, substitute, *files, **kwargs)
  
          with working_dir('spack-build/redist'):
              files = [
                  'pyflow-1.1.18/src/pyflow.py',
              ]
              filter_file(match, substitute, *files, **kwargs)
  