scout-gear=/$PWD filter="*.rb *.yaml" {
 Rakefile
 bin=bin filter="*"{
  scout
 }
 scout_commands=scout_commands filter="*"{
  rbbt
  alias
  find
  glob
  doc
  update
  template
  offsite
  workflow=workflow{
   task
   list
   info
   install
  }
  resource=resource{
   produce
  }
 }
 lib=lib {
  scout-gear.rb
  workflow-scout.rb
  rbbt-scout.rb
  scout.rb
  scout=scout{
   meta_extension.rb
   exceptions.rb

   misc.rb
   misc=misc{
    format.rb
    insist.rb
    digest.rb
    filesystem.rb
    monitor.rb
    system.rb
   }
   named_array.rb
   indiferent_hash.rb
   indiferent_hash=indiferent_hash{
    case_insensitive.rb
    options.rb
   }
   log.rb
   log=log{
    color.rb
    color_class.rb
    fingerprint.rb
    progress.rb
    progress=progress{
     report.rb
     util.rb
    }
    trap.rb
   }
   tmpfile.rb
   simple_opt.rb
   simple_opt=simple_opt{
    accessor.rb
    doc.rb
    parse.rb
    get.rb
    setup.rb
   }
   path.rb
   path=path{
    find.rb
    util.rb
    tmpfile.rb
   }
   concurrent_stream.rb
   cmd.rb
   open.rb
   open=open{
    lock.rb
    lock=lock{
     lockfile.rb
    }
    stream.rb
    remote.rb
    util.rb
   }
   resource.rb
   resource=resource{
    produce.rb
    produce=produce{
     rake.rb
    }
    software.rb
    scout.rb
    util.rb
    path.rb
   }
   config.rb
   persist.rb
   persist=persist{
    serialize.rb
    open.rb
    path.rb
   }
   workflow.rb
   workflow=workflow{
    definition.rb
    documentation.rb
    usage.rb
    util.rb
    step.rb
    step=step{
     config.rb
     dependencies.rb
     file.rb
     info.rb
     load.rb
     progress.rb
     provenance.rb
     status.rb
     inputs.rb
    }
    task.rb
    task=task{
     dependencies.rb
     inputs.rb
    }
    deployment.rb
    deployment=deployment{
     orchestrator.rb
    }
   }
   semaphore.rb
   work_queue.rb
   work_queue=work_queue{
    socket.rb
    worker.rb
   }
   tsv.rb
   tsv=tsv{
    util.rb
    util=util{
     process.rb
     select.rb
     process.rb
     unzip.rb
     reorder.rb
    }
    parser.rb
    dumper.rb
    transformer.rb
    persist.rb
    persist=persist{
     adapter.rb
     serialize.rb
     sdbm.rb
     tkrzw.rb
     tokyocabinet.rb
     fix_width_table.rb
    }
    index.rb
    traverse.rb
    attach.rb
    change_id.rb
    path.rb
    stream.rb
    open.rb
   }
   offsite.rb
   offsite=offsite{
    ssh.rb
    sync.rb
    step.rb
   }
   hpc=hpc{
    slurm.rb
   }
  }
 }
 test=test {
  test_helper.rb
  test_scout-gear.rb
  scout=scout{
   test_cmd.rb
   test_concurrent_stream.rb
   test_config.rb
   test_indiferent_hash.rb
   test_log.rb
   test_meta_extension.rb
   test_misc.rb
   test_named_array.rb
   test_open.rb
   test_path.rb
   test_persist.rb
   test_resource.rb
   test_semaphore.rb
   test_tmpfile.rb
   test_tsv.rb
   test_work_queue.rb
   test_workflow.rb
   workflow=workflow{
    test_definition.rb
    test_documentation.rb
    test_step.rb
    test_task.rb
    test_usage.rb
    test_util.rb
    step=step{
     test_dependencies.rb
     test_info.rb
     test_load.rb
     test_provenance.rb
     test_status.rb
    }
    task=task{
     test_dependencies.rb
     test_inputs.rb
    }
   }
   indiferent_hash=indiferent_hash{
    test_case_insensitive.rb
    test_options.rb
   }
  }
 }
 share=share{
  software=software{
   install_helpers
  }
  templates=templates{
   workflow.rb
  }
 }



 modules=modules{
  rbbt-util=rbbt-util filter="*.rb *.rake Rakefile *.rdoc *.R *.sh *.js *.haml *.sass *.txt *.conf LICENSE" {
   Migration-1.9.txt
   Troubleshooting.txt
   ToDo.txt
   Rakefile
   LICENSE
   README.rdoc
   bin=bin filter="*" {
    excel2tsv.rb
    rbbt
    rbbt_Rutil.rb
    rbbt_dangling_locks.rb
    rbbt_exec.rb
    rbbt_query.rb
    rbbt_find.rb
   }
   lib=lib{
    rbbt.rb

    rbbt-util.rb

    rbbt=rbbt{
     refactor.rb

     util=util{
      misc.rb
      misc=misc{
       refactor.rb

       serialize.rb
       exceptions.rb
       concurrent_stream.rb
       indiferent_hash.rb
       pipes.rb
       format.rb
       omics.rb
       inspect.rb
       math.rb
       development.rb
       lock.rb
       options.rb
       system.rb
       objects.rb
       manipulation.rb
       bgzf.rb
       multipart_payload.rb
       annotated_module.rb
       communication.rb
      }
      version.rb
      tar.rb
      color.rb
      colorize.rb
      named_array.rb
      cmd.rb
      docker.rb
      config.rb
      log.rb
      log=log{
       refactor.rb
       progress.rb
       progress=progress{
        util.rb
        report.rb
       }
      }
      open.rb
      semaphore.rb

      simpleopt.rb
      simpleopt=simpleopt{
       accessor.rb
       doc.rb
       parse.rb
       get.rb
       setup.rb
      }

      ssh.rb

      simpleDSL.rb

      chain_methods.rb

      tmpfile.rb
      tc_cache.rb
      filecache.rb

      R.rb
      R=R{
       eval.rb
       model.rb
       plot.rb
      }

      python.rb
      python=python{
       util.rb
      }

      excel2tsv.rb

      concurrency.rb
      concurrency=concurrency{
       processes.rb
       threads.rb
       processes=processes{
        socket.rb
        worker.rb
       }
      }

      procpath.rb

      migrate.rb
     }

     monitor.rb

     workflow.rb
     workflow=workflow{
      refactor.rb
      annotate.rb

      definition.rb
      dependencies.rb

      accessor.rb

      task.rb

      step.rb
      step=step{
       accessor.rb
       dependencies.rb
       info.rb
       prepare.rb
       run.rb
       save_load_inputs.rb
       status.rb
      }

      examples.rb
      doc.rb
      usage.rb

      soap.rb

      util=util{
       archive.rb
       provenance.rb
       orchestrator.rb
       trace.rb
       data.rb
      }

      remote_workflow.rb
      remote_workflow=remote_workflow{
       driver.rb
       driver=driver{
        rest.rb
        ssh.rb
       }

       remote_step.rb
       remote_step=remote_step{
        rest.rb
        ssh.rb
       }
      }

      integration=integration{
       cromwell.rb
       nextflow.rb
       ansible.rb
       ansible=ansible{
        workflow.rb
       }
      }
     }

     hpc.rb
     hpc=hpc{
      old=old{
       slurm.rb
      }
      orchestrate.old.rb

      batch.rb
      slurm.rb
      lsf.rb

      orchestrate.rb
      orchestrate=orchestrate{
       rules.rb
       chains.rb
       batches.rb
      }
      trace.rb
     }

     tsv.rb
     tsv=tsv{
      refactor.rb
      parser.rb
      dumper.rb

      matrix.rb

      accessor.rb
      util.rb
      marshal.rb
      serializers.rb
      manipulate.rb
      index.rb
      stream.rb
      attach.rb
      attach=attach{
       util.rb
      }
      melt.rb
      excel.rb
      csv.rb
      filter.rb
      field_index.rb
      change_id.rb
      parallel.rb
      parallel=parallel{
       traverse.rb
       through.rb
      }
     }

     packed_index.rb
     fix_width_table.rb

     persist.rb
     persist=persist{
      refactor.rb
      tsv.rb
      tsv=tsv{
       adapter.rb

       sharder.rb
       tokyocabinet.rb
       tokyocabinet=tokyocabinet{
        marshal.rb
       }
       fix_width_table.rb
       packed_index.rb
       kyotocabinet.rb
       lmdb.rb
       cdb.rb
       leveldb.rb
      }
     }

     resource.rb
     resource=resource{
      path.rb
      path=path{
       refactor.rb
      }
      util.rb
      with_key.rb
      rake.rb
     }

     annotations.rb
     annotations=annotations{
      util.rb
      annotated_array.rb
     }

     entity.rb
     entity=entity{
      identifiers.rb
     }

     association.rb
     association=association{
      util.rb
      database.rb
      open.rb
      index.rb
      item.rb
     }

     knowledge_base.rb
     knowledge_base=knowledge_base{
      enrichment.rb
      entity.rb
      query.rb
      registry.rb
      syndicate.rb
      traverse.rb
     }
    }
   }
   test=test {
    test_helper.rb
    data=data filter="*"{
     Test.xls
     dose_response
     dose_response2
     dose_response3
     example.pdf
     gene_ages
     identifiers
     test.tsv
    }
    rbbt=rbbt{
     test_annotations.rb
     test_association.rb
     test_entity.rb
     test_fix_width_table.rb
     test_knowledge_base.rb
     test_monitor.rb
     test_packed_index.rb
     test_persist.rb
     test_resource.rb
     test_tsv.rb
     test_workflow.rb
     resource=resource{
      test_path.rb
     }
     workflow=workflow{
      test_soap.rb
      test_doc.rb
      test_step.rb
      test_task.rb
     }
     association=association{
      test_database.rb
      test_index.rb
      test_item.rb
      test_open.rb
      test_util.rb
     }
     knowledge_base=knowledge_base{
      test_enrichment.rb
      test_query.rb
      test_registry.rb
     }
     persist=persist{
      tsv=tsv{
       test_cdb.rb
       test_kyotocabinet.rb
       test_leveldb.rb
       test_lmdb.rb
       test_sharder.rb
       test_tokyocabinet.rb
      }
      test_tsv.rb
     }
     tsv=tsv{
      test_accessor.rb
      test_attach.rb
      test_change_id.rb
      test_csv.rb
      test_excel.rb
      test_field_index.rb
      test_filter.rb
      test_index.rb
      test_manipulate.rb
      test_matrix.rb
      test_parallel.rb
      test_parser.rb
      test_stream.rb
      test_util.rb
      parallel=parallel{
       test_through.rb
       test_traverse.rb
      }
     }
     entity=entity{
      test_identifiers.rb
     }
     util=util{
      test_R.rb
      test_chain_methods.rb
      test_cmd.rb
      test_colorize.rb
      test_concurrency.rb
      test_config.rb
      test_excel2tsv.rb
      test_filecache.rb
      test_log.rb
      test_misc.rb
      test_open.rb
      test_python.rb
      test_semaphore.rb
      test_simpleDSL.rb
      test_simpleopt.rb
      test_tmpfile.rb
      R=R{
       test_eval.rb
       test_model.rb
       test_plot.rb
      }
      misc=misc{
       test_bgzf.rb
       test_format.rb
       test_lock.rb
       test_multipart_payload.rb
       test_omics.rb
       test_pipes.rb
      }
      simpleopt=simpleopt{
       test_get.rb
       test_parse.rb
       test_setup.rb
      }
      concurrency=concurrency{
       test_processes.rb
       test_threads.rb
      }
     }
    }
   }
   python=python filter="*"{
    rbbt.py
   }
   integration_test=integration_test{
    test_bed.rb
    test_helper.rb
    test_namespaces.rb
    test_workflow.rb
   }
   etc=etc filter="*"{
    app.d=app.d{
     init.rb

     base.rb

     requires.rb
     entities.rb
     finder.rb
     foundation.rb
     grid_system.rb
     knowledge_bases.rb
     resources.rb
     workflows.rb
     semaphores.rb
     remote_workflow_tasks.rb
    }
   }
   share=share{
    config.ru
    workflow_config.ru
    unicorn.rb
    color=color filter="*"{
     diverging_colors.hex
     color_names
    }
    rbbt_commands=rbbt_commands filter="*"{
     alias
     ansible
     check_bgzf
     cmd
     color
     log
     migrate
     migrate_job
     purge_job
     rsync
     watch
     system=system{
      clean
      deleted_files
      optimize
      purge
      report
      status
     }
     conf=conf{
      web_user=web_user{
       add
       list
       remove
      }
     }
     resource=resource{
      exists
      find
      glob
      get
      produce
      read
     }
     workflow=workflow{
      archive
      archive_all
      cmd
      example
      forget_deps
      info
      write_info
      init
      install
      jobs
      knowledge_base
      list
      monitor
      prov
      server
      task
      trace
      remote=remote{
       add
       list
       remove
      }
     }
     hpc=hpc{
      task
      orchestrate
      tail
      list
      clean
     }
     app=app{
      install
      start
      template
     }
     association=association{
      subset
     }
     tsv=tsv{
      assemble_pdf_table
      attach
      change_id
      collapse
      get
      head
      info
      json
      keys
      query
      read
      read_excel
      slice
      sort
      subset
      select
      transpose
      uncollapse
      unzip
      values
      write_excel
      zip
      view
     }
     stat=stat{
      abs
      boxplot
      compare_lists
      density
      heatmap
      log
      pvalue.qqplot
     }
     study=study{
      maf2study
      task
     }
     file_server=file_server{
      add
      list
      remove
     }
     benchmark=benchmark{
      pthrough
      throughput
      tsv
     }
    }
    Rlib=Rlib{
     plot.R
     svg.R
     util.R
    }
    software=install/software filter="*"{
     zran=zran{
      zran.c
     }
     lib=lib{
      install_helpers
     }
    }
   }
  }

 }
}