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 an API token

The Arvados API token is a secret key that enables the Arvados command line tools to authenticate themselves.

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: Getting started at the command line Next: Checking your environment

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.