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Getting started

  • Installation

Workflow users

  • Deploy workflows
  • Register input data

Workflow developers

  • Update conda environment files
  • Pin/lock conda environments
  • Update Snakemake wrappers

Snakemake developers

  • Scaffold Snakemake Plugins

API Reference

  • The Snakedeploy API
  • Internal API
Snakedeploy documentation
/
Internal API

Internal API

These pages document the entire internal API of Snakedeploy.

  • snakedeploy package
    • Submodules
    • snakedeploy.client module
      • get_parser()
      • main()
    • snakedeploy.providers module
      • Github
        • Github.checkout()
        • Github.clone()
        • Github.get_raw_file()
        • Github.get_source_file_declaration()
        • Github.matches()
        • Github.name
      • Gitlab
        • Gitlab.get_raw_file()
      • Local
        • Local.checkout()
        • Local.clone()
        • Local.get_raw_file()
        • Local.get_source_file_declaration()
        • Local.matches()
      • Provider
        • Provider.checkout()
        • Provider.clone()
        • Provider.get_raw_file()
        • Provider.get_repo_name()
        • Provider.matches()
      • get_provider()
    • snakedeploy.logging module
      • ColorizingStreamHandler
        • ColorizingStreamHandler.BLACK
        • ColorizingStreamHandler.BLUE
        • ColorizingStreamHandler.BOLD_SEQ
        • ColorizingStreamHandler.COLOR_SEQ
        • ColorizingStreamHandler.CYAN
        • ColorizingStreamHandler.GREEN
        • ColorizingStreamHandler.MAGENTA
        • ColorizingStreamHandler.RED
        • ColorizingStreamHandler.RESET_SEQ
        • ColorizingStreamHandler.WHITE
        • ColorizingStreamHandler.YELLOW
        • ColorizingStreamHandler.can_color_tty()
        • ColorizingStreamHandler.colors
        • ColorizingStreamHandler.decorate()
        • ColorizingStreamHandler.emit()
        • ColorizingStreamHandler.is_tty
      • Logger
        • Logger.cleanup()
        • Logger.debug()
        • Logger.error()
        • Logger.exit()
        • Logger.handler()
        • Logger.info()
        • Logger.location()
        • Logger.progress()
        • Logger.set_level()
        • Logger.set_stream_handler()
        • Logger.shellcmd()
        • Logger.text_handler()
        • Logger.warning()
      • setup_logger()

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