default:


  XSeeker_path: "/XSeeker"
  input_directory: "{{XSeeker_path}}/input/"


  galaxy:
    active: TRUE
    export_directory: "{{XSeeker_path}}/output/"
    export_method: "directory"


  database:
    base_data: "{{XSeeker_path}}/data/base.sql"
    recreate: FALSE
    models: 
      adduct
      cluster
      compound
      feature
      instrument
      instrument_config
      project
      sample
      smol_xcms_set
      software
      camera_parameters
      pairing_parameters
      peak_picking_parameters
      alignmenmt_parameters
    models_definition_path: "{{XSeeker_path}}/config/models.R"
    connection:
      connector: "SQLite"
      dbname: "{{XSeeker_path}}/test.sqlite"


  shiny:
    host: "0.0.0.0"
    port: 8765
    show_errors: TRUE
    appname: "XSeeker"
    base_ui_path: "{{XSeeker_path}}/R/base_ui.R"
    added_resources:
      www: "{{XSeeker_path}}/www/"
      sbs: "{{XSeeker_path}}/dist/shinyBS/www/"


  modules:
    checksums_file: "{{XSeeker_path}}/.checksums"
    re_compile_modified: FALSE
    sources_location: "{{XSeeker_path}}/modules"
    binaries_location: "{{XSeeker_path}}/bin"
    binaries:
      XSeekerRdataManager
      XSeekerFilePreProcessing
      XSeekerPreProcessPeakPicking
      XSeekerPreProcessAlignment
      XSeekerPreProcessCamera
      XSeekerKMDPlot
      XSeekerComputeFormula
      XSeekerChromatoAndMassSpectrum
      XSeekerClusterTable
      XSeekerDatabaseManager
      XSeekerDatabaseSummary
      XSeekerHairyPlotter
      XSeekerGalaxyInterfacR

    sources:


  XSeekerRdataManager:
    autoload: TRUE
    download_rdata_mzml_from_galaxy: FALSE


production:

  database:
    recreate: FALSE
    connection:
      connector: "SQLite"
      dbname: "{{XSeeker_path}}/production.sqlite"

  modules:
    re_compile_modified: FALSE


docker:

  database:
    recreate: TRUE
    connection:
      connector: "SQLite"
      dbname: "file::memory:"

  modules:
    re_compile_modified: FALSE