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| ``training_fill_data_library`` command | ||
| ====================================== | ||
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| This section is auto-generated from the help text for the planemo command | ||
| ``training_fill_data_library``. This help message can be generated with ``planemo training_fill_data_library | ||
| --help``. | ||
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| **Usage**:: | ||
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| planemo training_fill_data_library [OPTIONS] TOOL_PATH | ||
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| **Help** | ||
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| Build training template from workflow. | ||
| **Options**:: | ||
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| --topic_name TEXT Name (directory name) of the topic to create or in which | ||
| a tutorial should be created or updates [required] | ||
| --tutorial_name TEXT Name (directory name) of the tutorial to modify | ||
| [required] | ||
| --zenodo_link TEXT Zenodo URL with the input data | ||
| --datatypes PATH YAML file with the correspondance between Zenodo | ||
| extension and Galaxy datatypes | ||
| --help Show this message and exit. | ||
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| ``training_generate_from_wf`` command | ||
| ====================================== | ||
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| This section is auto-generated from the help text for the planemo command | ||
| ``training_generate_from_wf``. This help message can be generated with ``planemo training_generate_from_wf | ||
| --help``. | ||
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| **Usage**:: | ||
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| planemo training_generate_from_wf [OPTIONS] TOOL_PATH | ||
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| **Help** | ||
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| Create tutorial skeleton from workflow. | ||
| **Options**:: | ||
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| --topic_name TEXT Name (directory name) of the topic to create | ||
| or in which a tutorial should be created or | ||
| updates [required] | ||
| --tutorial_name TEXT Name (directory name) of the tutorial to | ||
| modify [required] | ||
| --workflow PATH Workflow of the tutorial (locally) | ||
| --galaxy_url TEXT URL of a Galaxy instance with the workflow | ||
| --galaxy_api_key TEXT API key on the Galaxy instance with the | ||
| workflow | ||
| --workflow_id TEXT ID of the workflow on the Galaxy instance | ||
| --galaxy_root DIRECTORY Root of development galaxy directory to | ||
| execute command with. | ||
| --galaxy_database_seed PATH Preseeded Galaxy sqlite database to target. | ||
| --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 or | ||
| instance 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). | ||
| --mulled_containers, --biocontainers | ||
| Test tools against mulled containers (forces | ||
| --docker). | ||
| --job_config_file PATH Job configuration file for Galaxy to target. | ||
| --tool_dependency_dir DIRECTORY | ||
| Tool dependency dir for Galaxy to target. | ||
| --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 aritfacts 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. | ||
| --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 PATH | ||
| 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 PATH Location of conda executable. | ||
| --conda_debug Enable more verbose conda logging. | ||
| --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_copy_dependencies Conda dependency resolution for Galaxy will | ||
| copy dependencies instead of attempting to | ||
| link them. | ||
| --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. | ||
| --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 PATH 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. | ||
| --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. | ||
| --help Show this message and exit. | ||
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