--- # 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:" is converted to the resource document with that resource # path. "resource:admin" uses the default admin, "resourceid:" 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