.vimproject

rbbt-util=/$PWD 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{
   util=util{
    misc.rb
    misc=misc{
     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{
     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{
    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
     pycompss.rb
     ansible.rb
     ansible=ansible{
      workflow.rb
     }
    }
   }

   hpc.rb
   hpc=hpc{
    batch.rb
    slurm.rb
    lsf.rb
    pbs.rb

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

   tsv.rb
   tsv=tsv{
    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{
    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
    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="*"{
   CollecTRI.gz
   Test.xls
   dose_response
   dose_response2
   dose_response3
   example.pdf
   gene_ages
   identifiers
   nature
   pina
   sample_genes
   test.tsv
  }
  rbbt=rbbt{
   test_annotations.rb
   test_association.rb
   test_entity.rb
   test_fix_width_table.rb
   test_knowledge_base.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_doc.rb
    test_remote_workflow.rb
    test_schedule.rb
    test_step.rb
    test_task.rb
    util=util{
     test_archive.rb
     test_data.rb
     test_orchestrator.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_entity.rb
    test_query.rb
    test_registry.rb
    test_syndicate.rb
    test_traverse.rb
    }
   persist=persist{
    test_tsv.rb
    tsv=tsv{
     test_cdb.rb
     test_kyotocabinet.rb
     test_leveldb.rb
     test_lmdb.rb
     test_sharder.rb
     test_tokyocabinet.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_marshal.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_config.rb
    test_excel2tsv.rb
    test_filecache.rb
    test_log.rb
    test_migrate.rb
    test_misc.rb
    test_open.rb
    test_procpath.rb
    test_python.rb
    test_semaphore.rb
    test_simpleDSL.rb
    test_simpleopt.rb
    test_ssh.rb
    test_tmpfile.rb
    R=R{
     test_eval.rb
     test_model.rb
     test_plot.rb
    }
    misc=misc{
     test_bgzf.rb
     test_communication.rb
     test_development.rb
     test_format.rb
     test_indiferent_hash.rb
     test_lock.rb
     test_multipart_payload.rb
     test_omics.rb
     test_pipes.rb
     test_serialize.rb
    }
    simpleopt=simpleopt{
     test_get.rb
     test_parse.rb
     test_setup.rb
    }
    concurrency=concurrency{
     test_processes.rb
     test_threads.rb
     }
   }
   hpc=hpc{
    hpc_test_workflows.rb
    test_batch.rb
    test_hpc_test_workflows.rb
    test_orchestrate.rb
    test_pbs.rb
    test_slurm.rb
    orchestrate=orchestrate{
     test_batches.rb
     test_chains.rb
     test_rules.rb
    }
   }
  }
 }
 python=python filter="*"{
  rbbt=rbbt{
   __init__.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
    claims
   }
   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
   }
  }
 }
}