Arvados API
★ Only Publicly Available OpenAPI DocumentCloud InfrastructureContainer Orchestrationbearer104 EndpointsREST
For Agents
Run and manage Arvados biomedical compute: collections, container requests, workflows, groups, users, and access controls on an Arvados cluster.
Use for: I need to create a new Arvados collection, Submit a container request to run an analysis, List recent container runs on the cluster, Retrieve the logs for a specific container
Not supported: Does not handle clinical EHR data, billing, or external data warehouses — use for managing Arvados collections, container requests, workflows, and access only.
Jentic publishes the only available OpenAPI specification for Arvados API, keeping it validated and agent-ready. Arvados is an open-source platform for managing and analysing large-scale biomedical data. Its REST API spans 104 endpoints across collections, containers, container requests, workflows, groups, users, links, logs, virtual machines, keep services, authorized keys, computed permissions, vocabularies, and credentials. Use it to upload datasets, kick off containerised analyses, manage compute groups and access, and read execution logs and provenance.
Install Jentic One Beta
Connect the Arvados API to your agent
Jentic One is a self-hosted execution layer for AI agents. It lets your agent call the Arvados API, or any other public or private API you need. You set the rules, the agent never sees your credentials, and every call is logged.
Two steps, two machines. Install the instance in a safe environment, then register your agent from wherever it runs.
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Step 1: Jentic One Host machine
# On the machine that will host your Jentic One instance:
curl -fsSL https://raw.githubusercontent.com/jentic/jentic-one/main/tools/install.sh | sh2
Step 2: Agent machine
# On the machine where your agent runs (keep this separate from the instance):
curl -fsSL https://raw.githubusercontent.com/jentic/jentic-one/main/tools/install.sh | sh
jentic register # connects your agent to your Jentic One instanceJentic One is in public beta. The setup above keeps your agent separate from the instance, which is what you want before using real credentials: an agent running as the same OS user as Jentic One can read its stored keys directly. Just evaluating? A single local install is fine to start. See the secure deployment guide for the tiers.
Capabilities
What an agent can do with Arvados API.
Create and manage data collections, including provenance and trash/untrash operations
Submit container requests and inspect their containers and logs
Run and manage Arvados workflows on a cluster
Manage groups, users, and authorized SSH keys for cluster access
Issue and manage API client authorizations and credentials
Read computed permissions to audit who can access which collections
Manage virtual machines, keep services, and cluster configs
Use Cases
Patterns agents use Arvados API for, with concrete tasks.
★ Genomic Pipeline Execution
Submit genomic analysis pipelines to an Arvados cluster by creating an input collection, posting a container request that references the workflow, and polling the resulting container for completion. /arvados/v1/collections, /arvados/v1/container_requests, and /arvados/v1/containers expose the data, request, and execution layers needed end to end.
Create a collection containing the input FASTQ files via /arvados/v1/collections, then POST /arvados/v1/container_requests referencing the GATK workflow and the new collection's uuid
Cluster Access Management
Manage who can access an Arvados cluster by provisioning users in groups, registering authorized SSH keys, and issuing API client authorizations. /arvados/v1/users, /arvados/v1/groups, /arvados/v1/authorized_keys, and /arvados/v1/api_client_authorizations cover the typical onboarding flow for a new researcher.
Add user 'researcher@uni.edu' to group 'lab-2026', register their SSH key via /arvados/v1/authorized_keys, and create an API client authorization for their pipelines
Provenance and Audit Reporting
Build provenance and audit reports by reading /arvados/v1/collections/{uuid}/provenance, /arvados/v1/collections/{uuid}/used_by, /arvados/v1/logs, and /arvados/v1/computed_permissions. The combination tells you which collections fed into which analyses and who could access them — essential for biomedical compliance reviews.
For collection uuid 'abc-123', call /arvados/v1/collections/abc-123/provenance and /arvados/v1/collections/abc-123/used_by, then write the lineage graph to a CSV
Storage Hygiene Workflow
Maintain storage hygiene on an Arvados cluster by listing collections, identifying ones older than a retention threshold, and trashing them via /arvados/v1/collections/{uuid}/trash. The /untrash counterpart provides safe recovery if a researcher requests it before garbage collection runs.
List collections modified more than 365 days ago, trash each via /arvados/v1/collections/{uuid}/trash, and write a recovery list of uuids in case any need /untrash
Agent-Driven Analysis Submission via Jentic
Let a research assistant agent submit an analysis on a researcher's behalf. The agent searches Jentic for 'submit an Arvados container request', loads the schema for /arvados/v1/container_requests, and executes — without persisting the bearer token in the agent process.
Search Jentic for 'submit an Arvados container request', load the schema, and execute referencing workflow uuid 'wf-42' and input collection uuid 'col-99'
Key Endpoints
104 endpoints — jentic publishes the only available openapi specification for arvados api, keeping it validated and agent-ready.
METHOD
PATH
DESCRIPTION
GET
/arvados/v1/collections
List collections
GET
/arvados/v1/collections/{uuid}/provenance
Fetch a collection's provenance graph
GET
/arvados/v1/containers
List containers
GET
/arvados/v1/groups
List groups
GET
/arvados/v1/users
List users
GET
/arvados/v1/authorized_keys
List authorized SSH keys
GET
/arvados/v1/api_client_authorizations/current
Fetch the current API client authorization
GET
/arvados/v1/computed_permissions
Read computed permissions across the cluster
GET
/arvados/v1/collections
List collections
GET
/arvados/v1/collections/{uuid}/provenance
Fetch a collection's provenance graph
GET
/arvados/v1/containers
List containers
GET
/arvados/v1/groups
List groups
GET
/arvados/v1/users
List users
GET
/arvados/v1/authorized_keys
List authorized SSH keys
GET
/arvados/v1/api_client_authorizations/current
Fetch the current API client authorization
GET
/arvados/v1/computed_permissions
Read computed permissions across the cluster
Why Jentic?
Three things that make agents converge on Jentic-routed access.
Credential isolation
Arvados bearer tokens are stored encrypted in the Jentic vault and injected at execution. Tokens can be rotated via /arvados/v1/api_client_authorizations without redeploying agent code.
Intent-based discovery
Agents search Jentic by intent (e.g., 'submit an Arvados container request', 'list Arvados collections') and Jentic returns the matching operation with its input schema, so the agent doesn't have to navigate 104 endpoints by hand.
Time to first call
Direct Arvados integration: 3-5 days to handle auth, paging, and the breadth of 104 endpoints. Through Jentic: under an hour to wire up the operations a single agent actually needs.
Related APIs
Alternatives and complements available in the Jentic catalogue.
Complementary
GitHub API
GitHub hosts the workflow definitions (CWL/WDL) that Arvados runs
Pair when an agent needs to fetch a workflow definition from GitHub before submitting an Arvados container request that references it.
FAQs
Specific to using Arvados API through Jentic.
Why is there no official OpenAPI spec for Arvados API?
Arvados publishes a Discovery Document rather than an OpenAPI specification. Jentic generates and maintains an OpenAPI spec so that AI agents and developers can call Arvados API via structured tooling. It is validated against the live API and kept up to date. Get started at https://app.jentic.com/sign-up.
What authentication does the Arvados API use?
Arvados uses HTTP Bearer authentication. You pass an API token in the Authorization header. Tokens are managed via /arvados/v1/api_client_authorizations and the current token can be inspected via /arvados/v1/api_client_authorizations/current. Through Jentic, the token is stored encrypted in the vault and injected at execution.
Can I submit a container request through the Arvados API?
Yes. POST /arvados/v1/container_requests creates a request to run a containerised analysis. The corresponding container can then be inspected via /arvados/v1/containers/{uuid} and its logs read from /arvados/v1/logs.
What are the rate limits for the Arvados API?
Arvados clusters do not impose a fixed public per-second rate limit; throughput is bounded by cluster capacity and per-user quotas configured by the cluster admin. For automated pipelines, follow Arvados' guidance on bulk operations and prefer paginated reads over many small calls.
How do I list my Arvados collections through Jentic?
Run pip install jentic, then search Jentic with 'list Arvados collections', load the schema for GET /arvados/v1/collections, and execute. The response is paginated; pass limit and offset to walk the full list.
Can I trash and untrash collections through the API?
Yes. /arvados/v1/collections/{uuid}/trash moves a collection to trash and /arvados/v1/collections/{uuid}/untrash restores it. Final deletion happens after the cluster's configured trash lifetime expires.
How do I audit who has access to a collection?
Use GET /arvados/v1/computed_permissions to read the computed permission graph; combine with /arvados/v1/groups and /arvados/v1/users to resolve names. This is the supported way to produce access-audit reports for biomedical compliance.
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