serve commandΒΆ

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

Usage:

planemo serve [OPTIONS] TOOL_PATH

Help

Launch Galaxy instance with specified tools.

The Galaxy tool panel will include just the referenced tool or tools (by default all the tools in the current working directory) and the upload tool.

planemo will search parent directories to see if any is a Galaxy instance - but one can pick the Galaxy instance to use with the --galaxy_root option or force planemo to download a disposable instance with the --install_galaxy flag.

planemo will run the Galaxy instance in an existing virtualenv if one exists in a .venv directory in the specified --galaxy_root. Otherwise, the Galaxy instance will run in a clean virtualenv created in /tmp.

planemo uses temporarily generated config files and environment variables to attempt to shield this execution of Galaxy from manually launched runs against that same Galaxy root - but this may not be bullet proof yet, so please be careful and do not try this against a production Galaxy instance.

Options:

--galaxy_root DIRECTORY         Root of development galaxy directory to
                                execute command with.
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
                                Python version to start Galaxy under
--extra_tools PATH              Extra tool sources to include in Galaxy's tool
                                panel (file or directory). These will not be
                                linted/tested/etc... but they will be
                                available to workflows and for interactive
                                use.
--install_galaxy                Download and configure a disposable copy of
                                Galaxy from github.
--galaxy_branch TEXT            Branch of Galaxy to target (defaults to
                                master) if a Galaxy root isn't specified.
--galaxy_source TEXT            Git source of Galaxy to target (defaults to
                                the official galaxyproject github source if a
                                Galaxy root isn't specified.
--skip_venv                     Do not create or source a virtualenv
                                environment for Galaxy, this should be used to
                                preserve an externally configured virtual
                                environment or conda environment.
--no_cache_galaxy               Skip caching of Galaxy source and dependencies
                                obtained with --install_galaxy. Not caching
                                this results in faster downloads (no git) - so
                                is better on throw away instances such with
                                TravisCI.
--no_cleanup                    Do not cleanup temp files created for and by
                                Galaxy.
--galaxy_email TEXT             E-mail address to use when launching single-
                                user Galaxy server.
--docker / --no_docker          Run Galaxy tools in Docker if enabled.
--docker_cmd TEXT               Command used to launch docker (defaults to
                                docker).
--docker_sudo / --no_docker_sudo
                                Flag to use sudo when running docker.
--docker_host TEXT              Docker host to target when executing docker
                                commands (defaults to localhost).
--docker_sudo_cmd TEXT          sudo command to use when --docker_sudo is
                                enabled (defaults to sudo).
--docker_run_extra_arguments TEXT
                                Extra arguments to pass to docker run.
--mulled_containers, --biocontainers
                                Test tools against mulled containers (forces
                                --docker). Disables conda resolution unless
                                any conda option has been set explicitly.
--galaxy_startup_timeout INTEGER RANGE
                                Wait for galaxy to start before assuming
                                Galaxy did not start.  [x>=1]
--job_config_file FILE          Job configuration file for Galaxy to target.
--tool_dependency_dir DIRECTORY
                                Tool dependency dir for Galaxy to target.
--tool_data_path DIRECTORY      Directory where data used by tools is located.
                                Required if tests are run in docker and should
                                make use of external reference data.
--port INTEGER                  Port to serve Galaxy on (default is 9090).
--host TEXT                     Host to bind Galaxy to. Default is 127.0.0.1
                                that is restricted to localhost connections
                                for security reasons set to 0.0.0.0 to bind
                                Galaxy to all ports including potentially
                                publicly accessible ones.
--engine [galaxy|docker_galaxy|external_galaxy]
                                Select an engine to serve artifacts such as
                                tools and workflows. Defaults to a local
                                Galaxy, but running Galaxy within a Docker
                                container.
--non_strict_cwl                Disable strict validation of CWL.
--docker_galaxy_image TEXT      Docker image identifier for docker-galaxy-
                                flavor used if engine type is specified as
                                ``docker-galaxy``. Defaults to
                                quay.io/bgruening/galaxy.
--docker_extra_volume PATH      Extra path to mount if --engine docker or
                                `--biocontainers` or `--docker`.
--test_data DIRECTORY           test-data directory to for specified tool(s).
--tool_data_table PATH          tool_data_table_conf.xml file to for specified
                                tool(s).
--dependency_resolvers_config_file FILE
                                Dependency resolver configuration for Galaxy
                                to target.
--brew_dependency_resolution    Configure Galaxy to use plain brew dependency
                                resolution.
--shed_dependency_resolution    Configure Galaxy to use brewed Tool Shed
                                dependency resolution.
--no_dependency_resolution      Configure Galaxy with no dependency resolvers.
--conda_prefix DIRECTORY        Conda prefix to use for conda dependency
                                commands.
--conda_exec FILE               Location of conda executable.
--conda_channels, --conda_ensure_channels TEXT
                                Ensure conda is configured with specified
                                comma separated list of channels.
--conda_use_local               Use locally built packages while building
                                Conda environments.
--conda_dependency_resolution   Configure Galaxy to use only conda for
                                dependency resolution.
--conda_auto_install / --no_conda_auto_install
                                Conda dependency resolution for Galaxy will
                                attempt to install requested but missing
                                packages.
--conda_auto_init / --no_conda_auto_init
                                Conda dependency resolution for Galaxy will
                                auto install conda itself using miniconda if
                                not availabe on conda_prefix.
--simultaneous_uploads / --no_simultaneous_uploads
                                When uploading files to Galaxy for tool or
                                workflow tests or runs, upload multiple files
                                simultaneously without waiting for the
                                previous file upload to complete.
--check_uploads_ok / --no_check_uploads_ok
                                When uploading files to Galaxy for tool or
                                workflow tests or runs, check that the history
                                is in an 'ok' state before beginning tool or
                                workflow execution.
--profile TEXT                  Name of profile (created with the
                                profile_create command) to use with this
                                command.
--postgres                      Use postgres database type.
--database_type [postgres|postgres_docker|sqlite|auto]
                                Type of database to use for profile - 'auto',
                                'sqlite', 'postgres', and 'postgres_docker'
                                are available options. Use postgres to use an
                                existing postgres server you user can access
                                without a password via the psql command. Use
                                postgres_docker to have Planemo manage a
                                docker container running postgres. Data with
                                postgres_docker is not yet persisted past when
                                you restart the docker container launched by
                                Planemo so be careful with this option.
--postgres_psql_path TEXT       Name or or path to postgres client binary
                                (psql).
--postgres_database_user TEXT   Postgres username for managed development
                                databases.
--postgres_database_host TEXT   Postgres host name for managed development
                                databases.
--postgres_database_port TEXT   Postgres port for managed development
                                databases.
--file_path DIRECTORY           Location for files created by Galaxy (e.g.
                                database/files).
--database_connection TEXT      Database connection string to use for Galaxy.
--shed_tool_conf TEXT           Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT           Location of shed tools directory for Galaxy.
--galaxy_single_user / --no_galaxy_single_user
                                By default Planemo will configure Galaxy to
                                run in single-user mode where there is just
                                one user and this user is automatically logged
                                it. Use --no_galaxy_single_user to prevent
                                Galaxy from running this way.
--daemon                        Serve Galaxy process as a daemon.
--pid_file FILE                 Location of pid file is executed with
                                --daemon.
--ignore_dependency_problems    When installing shed repositories for
                                workflows, ignore dependency issues. These
                                likely indicate a problem but in some cases
                                may not prevent a workflow from successfully
                                executing.
--skip_client_build             Do not build Galaxy client when serving
                                Galaxy.
--shed_install / --no_shed_install
                                By default Planemo will attempt to install
                                repositories needed for workflow testing. This
                                may not be appropriate for production servers
                                and so this can disabled by calling planemo
                                with --no_shed_install.
--cwl                           Configure Galaxy for use with CWL tool. (this
                                option is experimental and will be replaced
                                when and if CWL support is merged into
                                Galaxy).
--cwl_galaxy_root DIRECTORY     Root of development galaxy directory to
                                execute command with (must be branch of Galaxy
                                with CWL support, this option is experimental
                                and will be replaced with --galaxy_root when
                                and if CWL support is merged into Galaxy.
--help                          Show this message and exit.