Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/planemo/commands/cmd_serve.py @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
| author | shellac |
|---|---|
| date | Sat, 02 May 2020 07:14:21 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.7/site-packages/planemo/commands/cmd_serve.py Sat May 02 07:14:21 2020 -0400 @@ -0,0 +1,43 @@ +"""Module describing the planemo ``serve`` command.""" +import click + +from planemo import options +from planemo.cli import command_function +from planemo.galaxy import galaxy_serve +from planemo.runnable import for_paths +from planemo.tools import uris_to_paths + + +@click.command('serve') +@options.optional_tools_arg(multiple=True, allow_uris=True) +@options.galaxy_serve_options() +@options.enable_cwl_option() +@options.galaxy_cwl_root_option() +@command_function +def cli(ctx, uris, **kwds): + """Launch Galaxy instance with specified tools. + + The Galaxy tool panel will include just the referenced tool or tools (by + default all the tools in the current working directory) and the upload + tool. + + planemo will search parent directories to see if any is a Galaxy instance + - but one can pick the Galaxy instance to use with the ``--galaxy_root`` + option or force planemo to download a disposable instance with the + ``--install_galaxy`` flag. + + ``planemo`` will run the Galaxy instance in an existing virtualenv if one + exists in a ``.venv`` directory in the specified ``--galaxy_root``. + Otherwise, the Galaxy instance will run in a clean virtualenv created in + ``/tmp``. + + ``planemo`` uses temporarily generated config files and environment + variables to attempt to shield this execution of Galaxy from manually + launched runs against that same Galaxy root - but this may not be bullet + proof yet, so please be careful and do not try this against a production + Galaxy instance. + """ + paths = uris_to_paths(ctx, uris) + runnables = for_paths(paths) + kwds['galaxy_skip_client_build'] = False + galaxy_serve(ctx, runnables, **kwds)