Arvados™ Docs
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  1. Welcome
    1. Welcome to Arvados™!
    2. Arvados Community and Getting Help
  2. Run a workflow using Workbench
    1. Accessing Arvados Workbench
    2. Running a workflow using Workbench
    3. Create a Workflow with Composer
  3. 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
    4. Checking your environment
    5. Getting an API token
  4. Working with data sets
    1. Uploading data
    2. Downloading data
    3. Accessing Keep from GNU/Linux
    4. Accessing Keep from OS X
    5. Accessing Keep from Windows
    6. How Keep works
    7. Keep collection lifecycle
    8. Using arv-copy
    9. Using storage classes
    10. Using collection versioning
  5. Running workflows at the command line
    1. Running an Arvados workflow
    2. Using arvados-cwl-runner
  6. Working with git repositories
    1. Adding a new Arvados git repository
    2. Working with an Arvados git repository
  7. Develop an Arvados workflow
    1. Introduction to Crunch
    2. Writing a CWL workflow
    3. Federated Multi-Cluster Workflows
    4. Best Practices for writing CWL
    5. Arvados CWL Extensions
    6. Customizing Crunch environment using Docker
  8. Reference
    1. Linking alternate login accounts
    2. Arvados SDK Examples
  9. Arvados License
    1. Arvados Free Software Licenses
    2. GNU Affero General Public License
    3. Apache License
    4. Creative Commons
  10. Obsolete documentation
    1. Running an Arvados pipeline
    2. Using arv-run
    3. Writing a pipeline template
    4. Tools for writing Crunch pipelines
    5. Writing a Crunch script
    6. Running on an Arvados cluster
    7. Concurrent Crunch tasks
    8. run-command reference
    9. Pipeline template reference
    10. Scripts provided by Arvados
    11. Querying the Metadata Database

Getting an API token

The Arvados API token is a secret key that enables the arv command line client to access Arvados with the proper permissions.

Access the Arvados Workbench using this link: https://playground.arvados.org/ (Replace the hostname portion with the hostname of your local Arvados instance if necessary.)

Open a shell on the system where you want to use the Arvados client. This may be your local workstation, or an Arvados virtual machine accessed with Webshell or SSH (instructions for Unix or Windows).

In the Arvados Workbench, click on the dropdown menu icon in the upper right corner of the top navigation menu to access the user settings menu, and click on the menu item Current token, which lists your current token and instructions to set up your environment.

Setting environment variables

The Current token page, accessed using the dropdown menu icon in the upper right corner of the top navigation menu, includes a command you may copy and paste directly into the shell. It will look something as the following.

HISTIGNORE=$HISTIGNORE:'export ARVADOS_API_TOKEN=*'
export ARVADOS_API_TOKEN=2jv9346o396exampledonotuseexampledonotuseexes7j1ld
export ARVADOS_API_HOST=pirca.arvadosapi.com
unset ARVADOS_API_HOST_INSECURE
  • The export command puts a local shell variable into the environment that will be inherited by child processes such as the arv client.

settings.conf

Arvados tools will also look for the authentication information in ~/.config/arvados/settings.conf. If you have already put the variables into the environment following the instructions above, you can use these commands to create an Arvados configuration file:

$ echo "ARVADOS_API_HOST=$ARVADOS_API_HOST" > ~/.config/arvados/settings.conf
$ echo "ARVADOS_API_TOKEN=$ARVADOS_API_TOKEN" >> ~/.config/arvados/settings.conf

.bashrc

Alternately, you may add the declarations of ARVADOS_API_HOST and ARVADOS_API_TOKEN to the ~/.bashrc file on the system on which you intend to use the Arvados client. If you have already put the variables into the environment following the instructions above, you can use these commands to append the environment variables to your ~/.bashrc:

$ echo "export ARVADOS_API_HOST=$ARVADOS_API_HOST" >> ~/.bashrc
$ echo "export ARVADOS_API_TOKEN=$ARVADOS_API_TOKEN" >> ~/.bashrc
Previous: Checking your environment Next: Uploading data

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.