Mercurial > repos > shellac > sam_consensus_v3
annotate 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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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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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) |