navsection: adminguide
title: Cheat Sheet
navorder: 1
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+...
h1. Cheat Sheet
navsection: adminguide
title: Overview
navorder: 0
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+...
{% include alert-stub.html %}
navmenu: Concepts
title: Authentication
navorder: 2
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+...
h1. Authentication
h3. Refresh the access code (optional)
-Access codes have a limited lifetime. A refresh token allows an application to request a new access token.
\ No newline at end of file
+Access codes have a limited lifetime. A refresh token allows an application to request a new access token.
navmenu: Concepts
title: Crunch scripts
navorder: 5
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+...
h2. Crunch scripts
navsection: api
title: API Reference
navorder: 0
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+...
h1. API Reference
navmenu: Concepts
title: REST methods
navorder: 3
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+...
h1. REST Methods
navmenu: API Methods
title: "api_client_authorizations"
navorder: 1
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+...
h1. api_client_authorizations
navmenu: API Methods
title: "api_clients"
navorder: 2
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+...
h1. api_clients
navmenu: API Methods
title: "authorized_keys"
navorder: 3
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+...
h1. authorized_keys
navmenu: API Methods
title: "collections"
navorder: 4
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+...
h1. collections
navmenu: API Methods
title: "groups"
navorder: 5
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+...
h1. groups
navmenu: API Methods
title: "humans"
navorder: 6
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+...
h1. humans
navmenu: API Methods
title: "job_tasks"
navorder: 7
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+...
h1. job_tasks
navmenu: API Methods
title: "jobs"
navorder: 8
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+...
h1. jobs
navmenu: API Methods
title: "keep_disks"
navorder: 9
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+...
h1. keep_disks
navmenu: API Methods
title: "links"
navorder: 10
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+...
h1. links
navmenu: API Methods
title: "logs"
navorder: 11
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+...
h1. logs
navmenu: API Methods
title: "nodes"
navorder: 12
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+...
h1. nodes
navmenu: API Methods
title: "pipeline_instances"
navorder: 13
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+...
h1. pipeline_instances
navmenu: API Methods
title: "pipeline_templates"
navorder: 14
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+...
h1. pipeline_templates
navmenu: API Methods
title: "repositories"
navorder: 15
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+...
h1. repositories
navmenu: API Methods
title: "specimens"
navorder: 16
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+...
h1. specimens
navmenu: API Methods
title: "traits"
navorder: 17
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h1. traits
navmenu: API Methods
title: "users"
navorder: 18
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+...
h1. users
navmenu: API Methods
title: "virtual_machines"
navorder: 19
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+...
h1. virtual_machines
navmenu: Concepts
title: "Permission model"
navorder: 6
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h1. Permission model
navmenu: Concepts
title: Resources
navorder: 4
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h1. Resources
navmenu: Schema
title: ApiClient
navorder: 2
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+...
h1. ApiClient
navmenu: Schema
title: ApiClientAuthorization
navorder: 1
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+...
h1. ApiClientAuthorization
navmenu: Schema
title: AuthorizedKey
navorder: 3
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+...
h1. AuthorizedKey
navmenu: Schema
title: Collection
navorder: 4
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+...
h1. Collection
navmenu: Schema
title: Commit
navorder: 6
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+...
h1. Commit
navmenu: Schema
title: CommitAncestor
navorder: 5
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+...
h1. CommitAncestor
navmenu: Schema
title: Group
navorder: 7
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+...
h1. Group
navmenu: Schema
title: Human
navorder: 8
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+...
h1. Human
navmenu: Schema
title: Job
navorder: 9
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+...
h1. Job
navmenu: Schema
title: JobTask
navorder: 10
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+...
h1. JobTask
navmenu: Schema
title: KeepDisk
navorder: 11
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+...
h1. KeepDisk
navmenu: Schema
title: Link
navorder: 12
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+...
h1. Link
navmenu: Schema
title: Log
navorder: 14
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+...
h1. Log
navmenu: Schema
title: Node
navorder: 15
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+...
h1. Node
navmenu: Schema
title: PipelineInstance
navorder: 16
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+...
h1. PipelineInstance
navmenu: Schema
title: PipelineTemplate
navorder: 17
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+...
h1. PipelineTemplate
navmenu: Schema
title: Repository
navorder: 18
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+...
h1. Repository
navmenu: Schema
title: Specimen
navorder: 19
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+...
h1. Specimen
navmenu: Schema
title: Trait
navorder: 20
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+...
h1. Trait
navmenu: Schema
title: User
navorder: 21
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+...
h1. User
navmenu: Schema
title: VirtualMachine
navorder: 22
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+...
h1. VirtualMachine
layout: default
navsection: top
title: Arvados | Documentation
----
+...
<div class="frontpagehero">
<div style="padding:100px 50px; margin-left:0px; margin-top:0px">
navsection: installguide
title: Install client libraries
navorder: 5
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+...
h1. Install client libraries
navsection: installguide
title: Create standard objects
navorder: 4
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+...
h1. Create standard objects
navsection: installguide
title: Install the Crunch dispatcher
navorder: 3
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+...
h1. Crunch setup
navmenu: Examples
title: "Crunch examples"
navorder: 30
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+...
h1. Crunch examples
navmenu: Getting Started
title: "Checking your environment"
navorder: 10
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+...
h1. Checking your environment
navmenu: Getting Started
title: Accessing an Arvados VM over ssh
navorder: 2
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+...
h1. Accessing an Arvados Virtual Machine over ssh
navmenu: Getting Started
title: Accessing Arvados Workbench
navorder: 1
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+...
h1. Accessing Arvados Workbench
Access the Arvados beta test instance available using this link:
navsection: userguide
title: Welcome to Arvados!
navorder: 0
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+...
h1. Welcome to Arvados!
navmenu: Reference
title: "Getting an API token"
navorder: 01
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+...
h1. Reference: Getting an API token
navmenu: Reference
title: "Crunch utility libraries"
navorder: 31
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+...
h1. Crunch utility libraries
navmenu: Reference
title: "Command line SDK"
navorder: 22
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+...
h1. Reference: Command line SDK
navmenu: Reference
title: "Python SDK"
navorder: 23
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+...
h1. Reference: Python SDK
navmenu: Tutorials
title: "Writing a Crunch script"
navorder: 13
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+...
h1. Tutorial: Writing a Crunch script
navmenu: Tutorials
title: "Using GATK with Arvados"
navorder: 16
----
+...
h1. Tutorial: Using GATK with Arvados
navmenu: Tutorials
title: "Debugging a Crunch script"
navorder: 14
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+...
h1. Tutorial: Debugging a Crunch script
navmenu: Tutorials
title: "Running a Crunch job"
navorder: 12
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+...
h1. Tutorial: Running a crunch job
navmenu: Tutorials
title: "Storing and Retrieving data using Arvados Keep"
navorder: 11
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+...
h1. Tutorial: Storing and Retrieving data using Arvados Keep
navmenu: Tutorials
title: "Constructing a Crunch pipeline"
navorder: 15
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+...
h1. Tutorial: Constructing a Crunch pipeline
navmenu: Tutorials
title: "Parallel Crunch tasks"
navorder: 15
----
+...
h1. Tutorial: Parallel Crunch tasks
navmenu: Tutorials
title: "Querying the Metadata Database"
navorder: 16
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+...
h1. Tutorial: Querying the Metadata Database