code: def get_genome_ref(genome_build, aligner, galaxy_base):
      
      ref_files = dict(
              bowtie = "bowtie_indices.loc",
              bwa = "bwa_index.loc",
              samtools = "sam_fa_indices.loc",
              maq = "bowtie_indices.loc")
      remap_fns = dict(
              maq = _remap_to_maq
              )
      out_info = []
      for ref_get in [aligner, "samtools"]:
          ref_file = os.path.join(galaxy_base, "tool-data", ref_files[ref_get])
          with open(ref_file) as in_handle:
              for line in in_handle:
                  if not line.startswith("#"):
                      parts = line.strip().split()
                      if parts[0] == "index":
                          parts = parts[1:]
                      if parts[0] == genome_build:
                          out_info.append(parts[-1])
                          break
          try:
              out_info[-1] = remap_fns[ref_get](out_info[-1])
          except KeyError:
              pass
          except IndexError:
              raise IndexError("Genome %s not found in %s" % (genome_build,
                  ref_file))
  
      if len(out_info) != 2:
          raise ValueError("Did not find genome reference for %s %s" %
                  (genome_build, aligner))
      else:
          return tuple(out_info)
docs: Retrieve the reference genome file location from galaxy configuration.