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annotate venv/lib/python2.7/site-packages/planemo/commands/cmd_brew.py @ 0:d67268158946 draft

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author bcclaywell
date Mon, 12 Oct 2015 17:43:33 -0400
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d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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1 import click
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2
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3 from planemo.cli import pass_context
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4 from planemo import options
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5
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6 from galaxy.tools.loader_directory import load_tool_elements_from_path
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7
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8 from galaxy.tools.deps.requirements import parse_requirements_from_xml
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9 from galaxy.tools.deps import brew_exts
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10 from galaxy.tools.deps import brew_util
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11 from galaxy.util import bunch
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12
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13
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14 @click.command('brew')
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15 @options.optional_tools_arg()
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16 @options.brew_option()
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17 @pass_context
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18 def cli(ctx, path, brew=None):
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19 """Install tool requirements using brew. (**Experimental**)
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20
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21 An experimental approach to versioning brew recipes will be used.
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22 See full discussion on the homebrew-science issues page here -
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23 https://github.com/Homebrew/homebrew-science/issues/1191. Information
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24 on the implementation can be found at
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25 https://github.com/jmchilton/platform-brew
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26 until a more permanent project home is setup.
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27 """
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28 for (tool_path, tool_xml) in load_tool_elements_from_path(path):
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29 ctx.log('Brewing requirements from tool %s',
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30 click.format_filename(tool_path))
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31 mock_args = bunch.Bunch(brew=brew)
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32 brew_context = brew_exts.BrewContext(mock_args)
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33 requirements, containers = parse_requirements_from_xml(tool_xml)
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34
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35 for recipe_context in brew_util.requirements_to_recipe_contexts(
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36 requirements,
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37 brew_context
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38 ):
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39 brew_exts.versioned_install(recipe_context)