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annotate env/lib/python3.7/site-packages/planemo/commands/cmd_mull.py @ 4:79f47841a781 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1 """Module describing the planemo ``mull`` command."""
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2 import click
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3 from galaxy.tool_util.deps.mulled.mulled_build import mull_targets
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4
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5 from planemo import options
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6 from planemo.cli import command_function
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7 from planemo.mulled import build_mull_target_kwds, collect_mulled_target_lists
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8
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9
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10 @click.command('mull')
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11 @options.optional_tools_arg(multiple=True)
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12 @options.recursive_option()
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13 @options.mulled_options()
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14 @options.conda_ensure_channels_option()
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15 @command_function
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16 def cli(ctx, paths, **kwds):
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17 """Build containers for specified tools.
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18
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19 Supplied tools will be inspected for referenced requirement packages. For
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20 each combination of requirements a "mulled" container will be built. Galaxy
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21 can automatically discover this container and subsequently use it to run
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22 or test the tool.
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23
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24 For this to work, the tool's requirements will need to be present in a known
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25 Conda channel such as bioconda (https://github.com/bioconda/bioconda-recipes).
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26 This can be verified by running ``planemo lint --conda_requirements`` on the
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27 target tool(s).
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28 """
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29 for mulled_targets in collect_mulled_target_lists(ctx, paths, recursive=kwds["recursive"]):
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30 mull_target_kwds = build_mull_target_kwds(ctx, **kwds)
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31 command = kwds["mulled_command"]
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32 mull_targets(mulled_targets, command=command, **mull_target_kwds)