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Update command docs.
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‎docs/commands.rst

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@@ -10,12 +10,16 @@ documentation describes these commands.
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.. include:: commands/brew.rst
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.. include:: commands/brew_env.rst
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.. include:: commands/brew_init.rst
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.. include:: commands/conda_env.rst
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.. include:: commands/conda_init.rst
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.. include:: commands/conda_install.rst
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.. include:: commands/config_init.rst
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.. include:: commands/cwl_run.rst
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.. include:: commands/cwl_script.rst
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.. include:: commands/dependency_script.rst
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.. include:: commands/docker_build.rst
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.. include:: commands/docker_shell.rst
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.. include:: commands/docs.rst
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.. include:: commands/lint.rst
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.. include:: commands/normalize.rst
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.. include:: commands/project_init.rst

‎docs/commands/conda_env.rst

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``conda_env`` command
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======================================
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This section is auto-generated from the help text for the planemo command
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``conda_env``. This help message can be generated with ``planemo conda_env
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--help``.
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**Usage**::
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planemo conda_env [OPTIONS] TOOL_PATH
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**Help**
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Source output to activate a conda environment for this tool.
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% . <(planemo conda_env bowtie2.xml)
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% which bowtie2
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TODO_PLACE_PATH_HERE
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**Options**::
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--conda_prefix DIRECTORY Conda prefix to use for conda dependency
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commands.
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--conda_exec PATH Location of conda executable.
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--conda_debug Enable more verbose conda logging.
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--conda_ensure_channels TEXT Ensure conda is configured with specified comma
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separated list of channels.
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--help Show this message and exit.
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‎docs/commands/conda_init.rst

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``conda_init`` command
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======================================
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This section is auto-generated from the help text for the planemo command
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``conda_init``. This help message can be generated with ``planemo conda_init
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--help``.
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**Usage**::
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planemo conda_init [OPTIONS]
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**Help**
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Download and install conda.
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This will download conda for managing dependencies for your platform
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using the appropriate Miniconda installer.
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By running this command, you are agreeing to the terms of the conda
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license a 3-clause BSD 3 license. Please review full license at
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http://docs.continuum.io/anaconda/eula.
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**Options**::
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--conda_prefix DIRECTORY Conda prefix to use for conda dependency
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commands.
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--conda_exec PATH Location of conda executable.
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--conda_debug Enable more verbose conda logging.
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--conda_ensure_channels TEXT Ensure conda is configured with specified comma
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separated list of channels.
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--help Show this message and exit.
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‎docs/commands/conda_install.rst

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``conda_install`` command
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======================================
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This section is auto-generated from the help text for the planemo command
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``conda_install``. This help message can be generated with ``planemo conda_install
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--help``.
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**Usage**::
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planemo conda_install [OPTIONS] TOOL_PATH
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**Help**
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Install conda packages for tool requirements.
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**Options**::
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--conda_prefix DIRECTORY Conda prefix to use for conda dependency
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commands.
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--conda_exec PATH Location of conda executable.
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--conda_debug Enable more verbose conda logging.
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--conda_ensure_channels TEXT Ensure conda is configured with specified comma
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separated list of channels.
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--help Show this message and exit.
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‎docs/commands/cwl_run.rst

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--galaxy_root DIRECTORY Root of development galaxy directory to
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execute command with.
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--galaxy_sqlite_database DIRECTORY
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Preseeded Galaxy sqlite database to target.
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--galaxy_database_seed PATH Preseeded Galaxy sqlite database to target.
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--install_galaxy Download and configure a disposable copy of
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Galaxy from github.
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--galaxy_branch TEXT Branch of Galaxy to target (defaults to
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master) if a Galaxy root isn't specified.
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--galaxy_source TEXT Git source of Galaxy to target (defaults to
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the official galaxyproject github source if a
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Galaxy root isn't specified.
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--skip_venv Do not create or source a virtualenv
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environment for Galaxy, this should be used or
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instance to preserve an externally configured
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virtual environment or conda environment.
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--no_cache_galaxy Skip caching of Galaxy source and dependencies
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obtained with --install_galaxy. Not caching
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this results in faster downloads (no git) - so
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is better on throw away instances such with
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TravisCI.
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--no_cleanup Do not cleanup temp files created for and by
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Galaxy.
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--galaxy_email TEXT E-mail address to use when launching single-
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user Galaxy server.
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--job_config_file PATH Job configuration file for Galaxy to target.
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--tool_dependency_dir DIRECTORY
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Tool dependency dir for Galaxy to target.
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--port INTEGER Port to serve Galaxy on (default is 9090).
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--host TEXT Host to bind Galaxy to. Default is 127.0.0.1
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that is restricted to localhost connections
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--dependency_resolvers_config_file PATH
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Dependency resolver configuration for Galaxy
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to target.
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--tool_dependency_dir DIRECTORY
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Tool dependency dir for Galaxy to target.
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--brew_dependency_resolution Configure Galaxy to use plain brew dependency
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resolution.
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--shed_dependency_resolution Configure Galaxy to use brewed Tool Shed
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dependency resolution.
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--conda_prefix DIRECTORY Conda prefix to use for conda dependency
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commands.
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--conda_exec PATH Location of conda executable.
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--conda_debug Enable more verbose conda logging.
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--conda_ensure_channels TEXT Ensure conda is configured with specified
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comma separated list of channels.
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--conda_dependency_resolution Configure Galaxy to use only conda for
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dependency resolution.
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--conda_copy_dependencies Conda dependency resolution for Galaxy will
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copy dependencies instead of attempting to
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link them.
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--conda_auto_install Conda dependency resolution for Galaxy will
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auto install will attempt to install requested
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but missing packages.
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--conda_auto_init Conda dependency resolution for Galaxy will
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auto install conda itself using miniconda if
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not availabe on conda_prefix.
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--profile TEXT Location of pid file is executed with
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--daemon.
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--file_path DIRECTORY Location for files created by Galaxy (e.g.
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database/files).
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--database_connection TEXT Database connection string to use for Galaxy.
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--shed_tool_conf TEXT Location of shed tools conf file for Galaxy.
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--shed_tool_path TEXT Location of shed tools directory for Galaxy.
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--extra_tools PATH Extra tool sources to include in Galaxy's tool
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panel (file or directory). These will not be
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linted/tested/etc... but they will be
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available to workflows and for interactive
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use.
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--daemon Serve Galaxy process as a daemon.
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--pid_file TEXT Location of pid file is executed with
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--daemon.
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--cwl_galaxy_root DIRECTORY Root of development galaxy directory to
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execute command with (must be branch of Galaxy
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with CWL support, this option is experimental

‎docs/commands/docker_build.rst

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**Help**
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Builds (and optionally caches Docker images) for tool Dockerfiles.
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Build (and optionally cache Docker images) for tool Dockerfiles.
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Loads the tool or tools referenced by ``TOOL_PATH`` (by default all tools
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in current directory), and ensures they all reference the same Docker image

‎docs/commands/docs.rst

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``docs`` command
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======================================
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This section is auto-generated from the help text for the planemo command
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``docs``. This help message can be generated with ``planemo docs
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--help``.
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**Usage**::
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planemo docs [OPTIONS]
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**Help**
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Open the Planemo documentation in a web browser.
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**Options**::
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--help Show this message and exit.
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‎docs/commands/lint.rst

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**Help**
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Check specified tool(s) for common errors and adherence to best
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practices.
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Check tools for common errors and adherence to best practices.
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**Options**::
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‎docs/commands/serve.rst

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--galaxy_root DIRECTORY Root of development galaxy directory to
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execute command with.
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--galaxy_sqlite_database DIRECTORY
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Preseeded Galaxy sqlite database to target.
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--galaxy_database_seed PATH Preseeded Galaxy sqlite database to target.
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--install_galaxy Download and configure a disposable copy of
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Galaxy from github.
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--galaxy_branch TEXT Branch of Galaxy to target (defaults to
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master) if a Galaxy root isn't specified.
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--galaxy_source TEXT Git source of Galaxy to target (defaults to
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the official galaxyproject github source if a
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Galaxy root isn't specified.
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--skip_venv Do not create or source a virtualenv
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environment for Galaxy, this should be used or
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instance to preserve an externally configured
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virtual environment or conda environment.
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--no_cache_galaxy Skip caching of Galaxy source and dependencies
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obtained with --install_galaxy. Not caching
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this results in faster downloads (no git) - so
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is better on throw away instances such with
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TravisCI.
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--no_cleanup Do not cleanup temp files created for and by
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Galaxy.
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--galaxy_email TEXT E-mail address to use when launching single-
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user Galaxy server.
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--job_config_file PATH Job configuration file for Galaxy to target.
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--tool_dependency_dir DIRECTORY
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Tool dependency dir for Galaxy to target.
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--port INTEGER Port to serve Galaxy on (default is 9090).
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--host TEXT Host to bind Galaxy to. Default is 127.0.0.1
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that is restricted to localhost connections
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--dependency_resolvers_config_file PATH
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Dependency resolver configuration for Galaxy
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to target.
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--tool_dependency_dir DIRECTORY
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Tool dependency dir for Galaxy to target.
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--brew_dependency_resolution Configure Galaxy to use plain brew dependency
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resolution.
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--shed_dependency_resolution Configure Galaxy to use brewed Tool Shed
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dependency resolution.
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--conda_prefix DIRECTORY Conda prefix to use for conda dependency
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commands.
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--conda_exec PATH Location of conda executable.
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--conda_debug Enable more verbose conda logging.
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--conda_ensure_channels TEXT Ensure conda is configured with specified
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comma separated list of channels.
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--conda_dependency_resolution Configure Galaxy to use only conda for
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dependency resolution.
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--conda_copy_dependencies Conda dependency resolution for Galaxy will
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copy dependencies instead of attempting to
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link them.
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--conda_auto_install Conda dependency resolution for Galaxy will
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auto install will attempt to install requested
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but missing packages.
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--conda_auto_init Conda dependency resolution for Galaxy will
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auto install conda itself using miniconda if
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not availabe on conda_prefix.
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--profile TEXT Location of pid file is executed with
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--daemon.
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--file_path DIRECTORY Location for files created by Galaxy (e.g.
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database/files).
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--database_connection TEXT Database connection string to use for Galaxy.
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--shed_tool_conf TEXT Location of shed tools conf file for Galaxy.
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--shed_tool_path TEXT Location of shed tools directory for Galaxy.
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--extra_tools PATH Extra tool sources to include in Galaxy's tool
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panel (file or directory). These will not be
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linted/tested/etc... but they will be
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available to workflows and for interactive
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use.
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--daemon Serve Galaxy process as a daemon.
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--pid_file TEXT Location of pid file is executed with
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--daemon.
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--cwl Configure Galaxy for use with CWL tool. (this
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option is experimental and will be replaced
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when and if CWL support is merged into

‎docs/commands/shed_lint.rst

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Check a Tool Shed repository for common problems.
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With the ``--tools`` flag, this command lints actual Galaxy tools
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in addition to tool shed artifacts.
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