scout-gear 6.0.0 → 7.2.0

data/.vimproject

@@ -18,6 +18,7 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
  lib=lib {
   scout-gear.rb
   workflow-scout.rb
+  rbbt-scout.rb
   scout.rb
   scout=scout{
    meta_extension.rb
@@ -30,7 +31,9 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
     digest.rb
     filesystem.rb
     monitor.rb
+    system.rb
    }
+   named_array.rb
    indiferent_hash.rb
    indiferent_hash=indiferent_hash{
     case_insensitive.rb
@@ -77,10 +80,12 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
     produce=produce{
      rake.rb
     }
+    software.rb
     scout.rb
     util.rb
     path.rb
    }
+   config.rb
    persist.rb
    persist=persist{
     serialize.rb
@@ -94,6 +99,10 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
     step=step{
      info.rb
      load.rb
+     file.rb
+     config.rb
+     dependencies.rb
+     provenance.rb
     }
     task.rb
     task=task{
@@ -109,6 +118,20 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
     socket.rb
     worker.rb
    }
+   tsv.rb
+   tsv=tsv{
+    parser.rb
+    dumper.rb
+    persist.rb
+    index.rb
+    persist=persist{
+     adapter.rb
+     tokyocabinet.rb
+    }
+    traverse.rb
+    util.rb
+    path.rb
+   }
   }
  }
  test=test {
@@ -122,6 +145,13 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
    test_tmpfile.rb
   }
  }
+ share=share{
+  software=software{
+   install_helpers
+  }
+ }
+
+
 
  modules=modules{
   rbbt-util=rbbt-util filter="*.rb *.rake Rakefile *.rdoc *.R *.sh *.js *.haml *.sass *.txt *.conf LICENSE" {
@@ -241,477 +271,480 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
       migrate.rb
      }
 
-   monitor.rb
+     monitor.rb
 
-   workflow.rb
-   workflow=workflow{
-    annotate.rb
+     workflow.rb
+     workflow=workflow{
+      annotate.rb
 
-    definition.rb
-    dependencies.rb
+      definition.rb
+      dependencies.rb
 
-    accessor.rb
+      accessor.rb
 
-    task.rb
+      task.rb
 
-    step.rb
-    step=step{
-     accessor.rb
-     dependencies.rb
-     info.rb
-     prepare.rb
-     run.rb
-     save_load_inputs.rb
-     status.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
+      examples.rb
+      doc.rb
+      usage.rb
 
-    soap.rb
+      soap.rb
 
-    util=util{
-     archive.rb
-     provenance.rb
-     orchestrator.rb
-     trace.rb
-     data.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_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
-     }
-    }
+       remote_step.rb
+       remote_step=remote_step{
+        rest.rb
+        ssh.rb
+       }
+      }
 
-    integration=integration{
-     cromwell.rb
-     nextflow.rb
-     ansible.rb
-     ansible=ansible{
-      workflow.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{
-    parser.rb
-    dumper.rb
+     hpc.rb
+     hpc=hpc{
+      old=old{
+       slurm.rb
+      }
+      orchestrate.old.rb
 
-    matrix.rb
+      batch.rb
+      slurm.rb
+      lsf.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
-    }
-   }
+      orchestrate.rb
+      orchestrate=orchestrate{
+       rules.rb
+       chains.rb
+       batches.rb
+      }
+      trace.rb
+     }
 
-   packed_index.rb
-   fix_width_table.rb
+     tsv.rb
+     tsv=tsv{
+      parser.rb
+      dumper.rb
 
-   persist.rb
-   persist=persist{
-    refactor.rb
-    tsv.rb
-    tsv=tsv{
-     adapter.rb
+      matrix.rb
 
-     sharder.rb
-     tokyocabinet.rb
-     tokyocabinet=tokyocabinet{
+      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
+      }
      }
-     fix_width_table.rb
+
      packed_index.rb
-     kyotocabinet.rb
-     lmdb.rb
-     cdb.rb
-     leveldb.rb
-    }
-   }
+     fix_width_table.rb
 
-   resource.rb
-   resource=resource{
-    path.rb
-    util.rb
-    with_key.rb
-    rake.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
+      }
+     }
 
-   annotations.rb
-   annotations=annotations{
-    util.rb
-    annotated_array.rb
-   }
+     resource.rb
+     resource=resource{
+      path.rb
+      path=path{
+       refactor.rb
+      }
+      util.rb
+      with_key.rb
+      rake.rb
+     }
 
-   entity.rb
-   entity=entity{
-    identifiers.rb
-   }
+     annotations.rb
+     annotations=annotations{
+      util.rb
+      annotated_array.rb
+     }
 
-   association.rb
-   association=association{
-    util.rb
-    database.rb
-    open.rb
-    index.rb
-    item.rb
-   }
+     entity.rb
+     entity=entity{
+      identifiers.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
+     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
+     }
     }
-   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
+   test=test {
+    test_helper.rb
+    data=data filter="*"{
+     Test.xls
+     dose_response
+     dose_response2
+     dose_response3
+     example.pdf
+     gene_ages
+     identifiers
+     test.tsv
     }
-   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
+    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
+      }
+     }
     }
    }
-   entity=entity{
-    test_identifiers.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
+    }
    }
-   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
+   share=share{
+    config.ru
+    workflow_config.ru
+    unicorn.rb
+    color=color filter="*"{
+     diverging_colors.hex
+     color_names
     }
-    misc=misc{
-     test_bgzf.rb
-     test_format.rb
-     test_lock.rb
-     test_multipart_payload.rb
-     test_omics.rb
-     test_pipes.rb
+    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
+     }
     }
-    simpleopt=simpleopt{
-     test_get.rb
-     test_parse.rb
-     test_setup.rb
+    Rlib=Rlib{
+     plot.R
+     svg.R
+     util.R
     }
-    concurrency=concurrency{
-     test_processes.rb
-     test_threads.rb
+    software=install/software filter="*"{
+     zran=zran{
+      zran.c
+     }
+     lib=lib{
+      install_helpers
      }
-   }
-  }
- }
- 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
-   }
-  }
- }
-}
 
  }
 }