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brew_env.rst

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brew_env command

This section is auto-generated from the help text for the planemo command brew_env. This help message can be generated with planemo brew_env --help.

Usage:

planemo brew_env [OPTIONS] TOOL_PATH

Help

List commands to inject brew dependencies.

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

% . <(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.

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

Options:

--brew PATH     Homebrew 'brew' executable to use.
--skip_install  Skip installation - only source requirements already
                available.
--shell
--help          Show this message and exit.