def cli(ctx, path, brew=None, skip_install=False, shell=None):
    """List commands to inject brew dependencies.

    Display commands used to modify environment to inject tool's brew
    dependencies.

    \b
        % . <(planemo brew_env bowtie2.xml)
        % which bowtie2
        /home/john/.linuxbrew/Cellar/bowtie2/2.1.0/bin/bowtie2

    By default this will attempt to attempt to install these recipes as needed.
    This automatic installation can be skipped with the ``--skip_install``
    flag.

    Intead of injecting the enviornment into your current shell using the above
    idiom, the ``--shell`` flag can be sent to launch a new subshell when
    sourced.

    \b
        % . <(planemo brew_env --skip_install --shell bowtie2.xml)
        (bowtie2) % which bowtie2
        /home/john/.linuxbrew/Cellar/bowtie2/2.1.0/bin/bowtie2

    """
    tool_xml = load_tool(path)
    mock_args = bunch.Bunch(brew=brew)
    brew_context = brew_exts.BrewContext(mock_args)
    requirements, containers = parse_requirements_from_xml(tool_xml)

    lines = []
    for recipe_context in brew_util.requirements_to_recipe_contexts(
        requirements,
        brew_context
    ):
        if not skip_install:
            brew_exts.versioned_install(recipe_context)
        lines = brew_exts.build_env_statements_from_recipe_context(
            recipe_context
        )
        split_lines = lines.split("\n")
        lines.extend(split_lines)
    if shell:
        # TODO: Would be cool if this wasn't a bunch of random hackery.
        launch_shell = os.environ.get("SHELL")
        if "bash" in launch_shell:
            ps1 = ps1_for_path(path)
            launch_shell = '(source ~/.bashrc; env PS1="%s" %s --norc)' % (
                ps1,
                launch_shell,
            )
        lines.extend([launch_shell])
        print(";".join(lines))
    else:
        print("\n".join(lines))
Exemple #2
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def cli(ctx, path, brew=None):
    """Install tool requirements using brew. (**Experimental**)

    An experimental approach to versioning brew recipes will be used.
    See full discussion on the homebrew-science issues page here -
    https://github.com/Homebrew/homebrew-science/issues/1191. Information
    on the implementation can be found at
    https://github.com/jmchilton/platform-brew
    until a more permanent project home is setup.
    """
    for (tool_path, tool_xml) in load_tool_elements_from_path(path):
        ctx.log('Brewing requirements from tool %s',
                click.format_filename(tool_path))
        mock_args = bunch.Bunch(brew=brew)
        brew_context = brew_exts.BrewContext(mock_args)
        requirements, containers = parse_requirements_from_xml(tool_xml)

        for recipe_context in brew_util.requirements_to_recipe_contexts(
                requirements, brew_context):
            brew_exts.versioned_install(recipe_context)
Exemple #3
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def cli(ctx, path, brew=None):
    """Install tool requirements using brew. (**Experimental**)

    An experimental approach to versioning brew recipes will be used.
    See full discussion on the homebrew-science issues page here -
    https://github.com/Homebrew/homebrew-science/issues/1191. Information
    on the implementation can be found at
    https://github.com/jmchilton/platform-brew
    until a more permanent project home is setup.
    """
    for (tool_path, tool_xml) in load_tool_elements_from_path(path):
        ctx.log('Brewing requirements from tool %s',
                click.format_filename(tool_path))
        mock_args = bunch.Bunch(brew=brew)
        brew_context = brew_exts.BrewContext(mock_args)
        requirements, containers = parse_requirements_from_xml(tool_xml)

        for recipe_context in brew_util.requirements_to_recipe_contexts(
            requirements,
            brew_context
        ):
            brew_exts.versioned_install(recipe_context)