Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/planemo/commands/cmd_mull.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_mull.py Sat May 02 07:14:21 2020 -0400 @@ -0,0 +1,32 @@ +"""Module describing the planemo ``mull`` command.""" +import click +from galaxy.tool_util.deps.mulled.mulled_build import mull_targets + +from planemo import options +from planemo.cli import command_function +from planemo.mulled import build_mull_target_kwds, collect_mulled_target_lists + + +@click.command('mull') +@options.optional_tools_arg(multiple=True) +@options.recursive_option() +@options.mulled_options() +@options.conda_ensure_channels_option() +@command_function +def cli(ctx, paths, **kwds): + """Build containers for specified tools. + + Supplied tools will be inspected for referenced requirement packages. For + each combination of requirements a "mulled" container will be built. Galaxy + can automatically discover this container and subsequently use it to run + or test the tool. + + For this to work, the tool's requirements will need to be present in a known + Conda channel such as bioconda (https://github.com/bioconda/bioconda-recipes). + This can be verified by running ``planemo lint --conda_requirements`` on the + target tool(s). + """ + for mulled_targets in collect_mulled_target_lists(ctx, paths, recursive=kwds["recursive"]): + mull_target_kwds = build_mull_target_kwds(ctx, **kwds) + command = kwds["mulled_command"] + mull_targets(mulled_targets, command=command, **mull_target_kwds)