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annotate env/lib/python3.7/site-packages/planemo/commands/cmd_brew.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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1 """Module describing the planemo ``brew`` command."""
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2 import click
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3 from galaxy.tool_util.deps import (
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4 brew_exts,
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5 brew_util,
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6 )
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7 from galaxy.tool_util.deps.requirements import parse_requirements_from_xml
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8 from galaxy.tool_util.loader_directory import load_tool_elements_from_path
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9 from galaxy.util import bunch
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10
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11 from planemo import options
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12 from planemo.cli import command_function
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13
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14
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15 @click.command('brew')
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16 @options.optional_tools_arg()
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17 @options.brew_option()
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18 @command_function
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19 def cli(ctx, path, brew=None):
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20 """Install tool requirements using brew.
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21
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22 An experimental approach to versioning brew recipes will be used.
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23 See full discussion on the homebrew-science issues page here -
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24 https://github.com/Homebrew/homebrew-science/issues/1191. Information
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25 on the implementation can be found at
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26 https://github.com/jmchilton/platform-brew
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27 until a more permanent project home is setup.
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28 """
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29 for (tool_path, tool_xml) in load_tool_elements_from_path(path):
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30 ctx.log('Brewing requirements from tool %s',
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31 click.format_filename(tool_path))
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32 mock_args = bunch.Bunch(brew=brew)
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33 brew_context = brew_exts.BrewContext(mock_args)
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34 requirements, containers = parse_requirements_from_xml(tool_xml)
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35
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36 for recipe_context in brew_util.requirements_to_recipe_contexts(
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37 requirements,
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38 brew_context
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39 ):
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40 brew_exts.versioned_install(recipe_context)