Mercurial > repos > shellac > sam_consensus_v3
view env/lib/python3.9/site-packages/planemo/commands/cmd_mull.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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"""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)