Arvados API

Name: Arvados API
Brand: Arvados API
Availability: InStock

★ 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.

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.

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 | sh

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 instance

Jentic 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

GET STARTED

Start building with Arvados API

Explore with Jentic

View OpenAPI Document

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.

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

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.

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.