| # The provision script can take a yaml file with provision options | |
| # This is a dictionary of command-line arguments for the provisioning script | |
| force: False | |
| samples: False | |
| sample-collection: Samples | |
| sample-folder: Images | |
| # Set use-defaults to False to skip default settings | |
| use-defaults: True | |
| # Set mongo_compat to False to not automatically set the mongo feature | |
| # compatibility version to the current server version. | |
| mongo-compat: True | |
| # A list of additional pip modules to install; if any are girder plugins with | |
| # client-side code, also specify rebuild-client. | |
| # pip: | |
| # - girder-oauth | |
| # - girder-ldap | |
| # rebuild-client may be False, True (for production mode), or "development" | |
| rebuild-client: False | |
| # Run additional shell commands before start | |
| # shell: | |
| # - ls | |
| # Default admin user if there are no admin users | |
| admin: | |
| login: admin | |
| password: password | |
| firstName: Admin | |
| lastName: Admin | |
| email: admin@nowhere.nil | |
| public: True | |
| # Default assetstore if there are no assetstores | |
| assetstore: | |
| method: createFilesystemAssetstore | |
| name: Assetstore | |
| root: /assetstore | |
| # Any resources to ensure exist. A model must be specified. This creates the | |
| # resource if there is no match for all specified values. A value of | |
| # "resource:<path>" is converted to the resource document with that resource | |
| # path. "resource:admin" uses the default admin, "resourceid:<path>" is the | |
| # string id for the resource path, and "resourceid:admin" is the string if for | |
| # default admin. | |
| # You can add metadata to a resource. The default key is meta. If | |
| # metadata_update is False, metadata will not be set if any metadata | |
| # already exists. | |
| resources: | |
| - model: collection | |
| name: Tasks | |
| creator: resource:admin | |
| public: True | |
| - model: folder | |
| parent: resource:collection/Tasks | |
| parentType: collection | |
| name: "Slicer CLI Web Tasks" | |
| creator: resource:admin | |
| public: True | |
| # metadata: | |
| # sample_key: sample_value | |
| # metadata_key: meta | |
| # metadata_update: True | |
| settings: | |
| worker.broker: "amqp://guest:guest@rabbitmq" | |
| worker.backend: "rpc://guest:guest@rabbitmq" | |
| worker.api_url: "http://girder:8080/api/v1" | |
| worker.direct_path: True | |
| core.brand_name: "Digital Slide Archive" | |
| histomicsui.webroot_path: "histomics" | |
| histomicsui.alternate_webroot_path: "histomicstk" | |
| histomicsui.delete_annotations_after_ingest: True | |
| homepage.markdown: |- | |
| # Digital Slide Archive | |
| --- | |
| ## Bioinformatics Platform | |
| Welcome to the **Digital Slide Archive**. | |
| Developers who want to use the Girder REST API should check out the | |
| [interactive web API docs](api/v1). | |
| The [HistomicsUI](histomics) application is enabled. | |
| slicer_cli_web.task_folder: "resourceid:collection/Tasks/Slicer CLI Web Tasks" | |
| # List slicer-cli-images to pull and load | |
| slicer-cli-image: | |
| - dsarchive/histomicstk:latest | |
| # The worker can specify parameters for provisioning | |
| # worker-rabbitmq-host: girder:8080 | |
| worker-rabbitmq-user: guest | |
| worker-rabbitmq-pass: guest | |
| worker-config: /opt/girder_worker/girder_worker/worker.local.cfg | |
| # These have precedence over the top level values | |
| worker: | |
| # rabbitmq-host: girder:8080 | |
| # rabbitmq-user: guest | |
| # rabbitmq-pass: guest | |
| # config: /opt/girder_worker/girder_worker/worker.local.cfg | |
| # Install additional pip packages in the worker | |
| # pip: | |
| # - package_one | |
| # Run additional shell commands in the worker before start | |
| # shell: | |
| # - ls | |