Arvados™ Docs
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  1. Welcome
    1. Welcome to Arvados™!
    2. Arvados Community and Getting Help
  2. Walkthough
    1. Processing Whole Genome Sequences
  3. Run a workflow using Workbench
    1. Accessing Arvados Workbench
    2. Running a workflow using Workbench
  4. Working at the Command Line
    1. Getting started at the command line
    2. Getting an API token
    3. Checking your environment
  5. Access an Arvados virtual machine
    1. Accessing an Arvados VM with Webshell
    2. Accessing an Arvados VM with SSH - Unix Environments
    3. Accessing an Arvados VM with SSH - Windows Environments
  6. Working with data sets
    1. Uploading data
    2. Downloading data
    3. Access Keep as a GNU/Linux filesystem
    4. Access Keep from macOS Finder
    5. Access Keep from Windows File Explorer
    6. Trashing and untrashing data
    7. Using arv-copy
    8. Using collection versioning
    9. Using storage classes
  7. Data Analysis with Workflows
    1. Starting a Workflow at the Command Line
    2. arvados-cwl-runner options
    3. Developing workflows with CWL
    4. Working with Docker images
    5. Guidelines for Writing High-Performance Portable Workflows
    6. Arvados CWL Extensions
    7. Federated Multi-Cluster Workflows
    8. CWL version support
    9. Analyzing workflow performance
  8. Working with git repositories
    1. Adding a new Arvados git repository
    2. Working with an Arvados git repository
  9. Reference
    1. Linking alternate login accounts
    2. Arvados SDK Examples
  10. Arvados License
    1. Arvados Free Software Licenses
    2. GNU Affero General Public License
    3. Apache License
    4. Creative Commons

Getting started at the command line

Many operations in Arvados can be performed using either the web Workbench or through command line tools. Some operations can only be done using the command line.

To use the command line tools, you can either log into an Arvados-managed VM instance where those tools are pre-installed, or install the Arvados tools on your own system.

To log into an Arvados-managed VM, see instructions for Webshell or Unix or Windows .

To install the Arvados tools on your own system, you should install the Command line SDK (requires Ruby) and Python SDK (requires Python). You may also want to install arvados-cwl-runner to submit workflows and arvados-fuse to mount keep as a filesystem.

Once you are logged in or have command line tools installed, see getting an API token and check your environment .

Previous: Running a workflow using Workbench Next: Getting an API token

The content of this documentation is licensed under the Creative Commons Attribution-Share Alike 3.0 United States licence.
Code samples in this documentation are licensed under the Apache License, Version 2.0.