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---
# 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: [email protected]
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
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