Module: MiGA::Cli::Base

Included in:
Defined in:

Constant Summary collapse

  generic: 'MiGA: The Microbial Genomes Atlas',
  # Workflows
  quality_wf: 'Evaluate the quality of input genomes',
  derep_wf: 'Dereplicate a collection of input genomes',
  classify_wf: 'Classify input genomes against a reference database',
  preproc_wf: 'Preprocess input genomes or metagenomes',
  index_wf: 'Generate distance indexing of input genomes',
  # Projects
  new: 'Create an empty MiGA project',
  about: 'Display information about a MiGA project',
  doctor: 'Perform consistency checks on a MiGA project',
  get_db: 'Download a pre-indexed database',
  browse: 'Explore a project locally using a web browser',
  # Datasets
  add: 'Create a dataset in a MiGA project',
  get: 'Download a dataset from public databases into a MiGA project',
  ncbi_get: 'Download all genomes in a taxon from NCBI into a MiGA project',
  gtdb_get: 'Download all genomes in a taxon from GTDB into a MiGA project',
  rm: 'Remove a dataset from a MiGA project',
  find: 'Find unregistered datasets based on result files',
  ln: 'Link datasets (including results) from one project to another',
  ls: 'List all registered datasets in a MiGA project',
  archive: 'Generate a tar-ball with all files from select datasets',
  # Results
  add_result: 'Register a result',
  stats: 'Extract statistics for the given result',
  files: 'List registered files from the results of a dataset or project',
  run: 'Execute locally one step analysis producing the given result',
  summary: 'Generate a summary table for the statistics of all datasets',
  next_step: 'Return the next task to run in a dataset or project',
  # Objects (Datasets or Projects)
  edit: 'Edit the metadata of a dataset or project',
  option: 'Get or set options of a dataset or project',
  touch: 'Change the "last modified" time to now without changes',
  # System
  init: 'Initialize MiGA to process new projects',
  daemon: 'Control the daemon of a MiGA project',
  lair: 'Control groups of daemons for several MiGA projects',
  date: 'Return the current date in standard MiGA format',
  console: 'Open an IRB console with MiGA',
  env: 'Shell code to load MiGA environment',
  # Taxonomy
  tax_set: 'Register taxonomic information for datasets',
  tax_test: 'Return test of taxonomic distributions for query datasets',
  tax_index: 'Create a taxonomy-indexed list of the datasets',
  tax_dist: 'Estimate distributions of distance by taxonomy',
  # Projects
  create_project: :new,
  project_info: :about,
  download: :get_db,
  # Datasets
  create_dataset: :add,
  download_dataset: :get,
  unlink_dataset: :rm,
  find_datasets: :find,
  import_datasets: :ln,
  list_datasets: :ls,
  # Results
  result_stats: :stats,
  list_files: :files,
  run_local: :run,
  sum_stats: :summary,
  next_task: :next_step,
  # Objects
  update_metadata: :edit,
  # System
  c: :console,
  # Taxonomy
  add_taxonomy: :tax_set,
  test_taxonomy: :tax_test,
  index_taxonomy: :tax_index,
  tax_distributions: :tax_dist,