Arvados™ Docs
  1. Welcome
    1. Welcome to Arvados™!
    2. Arvados Community and Getting Help
  2. Walkthough
    1. Accessing Arvados Workbench
    2. Processing Whole Genome Sequences
  3. Working at the Command Line
    1. Getting started at the command line
    2. Getting an API token
    3. Checking your environment
  4. Working with data sets
    1. Organizating data
    2. Uploading data
    3. Downloading data
    4. Trashing and untrashing data
    5. Using arv-copy
    6. Access Keep as a GNU/Linux filesystem
    7. Access Keep from macOS Finder
    8. Access Keep from Windows File Explorer
    9. Using collection versioning
    10. Using storage classes
  5. Data Analysis with Workflows
    1. Running a workflow using Workbench
    2. Starting a Workflow at the Command Line
    3. arvados-cwl-runner options
    4. Analyzing workflow performance
    5. Debugging workflows - shell access
    6. Analyzing workflow cost (cloud only)
    7. Federated Multi-Cluster Workflows
  6. Common Workflow Language
    1. Getting Started with CWL
    2. Developing CWL Workflows with VSCode
    3. Working with container images
    4. Guidelines for Writing High-Performance Portable Workflows
    5. CWL Resources
    6. Arvados CWL Extensions
    7. CWL version support
  7. 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
  8. Reference
    1. Workbench 2 migration
    2. Linking alternate login accounts
    3. Arvados SDK Examples
  9. 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 virtual machine where those tools are pre-installed, or install the Arvados tools on your own system.

Option 1: Using an Arvados virtual machine

This is the command line interface we recommend for most day-to-day work, because the tools are all preinstalled and preconfigured for you. You can log in to any virtual machine where you have permission by using:

Option 2: Installing Arvados tools on your own system

This option gives you more flexibility in your work, but takes more time to set up.

Configure Arvados package repositories for your system

Doing this isn’t strictly required for most tools, but will streamline the installation process. Follow the Arvados package repository instructions.

Install individual tool packages

Here are the client packages you can install on your system. You can skip any you don’t want or need except for the Python SDK (most other tools require it).

  • Python SDK: This provides an Arvados API client in Python, as well as low-level command line tools.
  • Command-line SDK: This provides the high-level arv command and user interface to the Arvados API.
  • FUSE Driver: This provides the arv-mount command and FUSE driver that lets you access Keep using standard Linux filesystem tools.
  • CWL Runner: This provides the arvados-cwl-runner command to register and run workflows in Crunch.
  • crunchstat-summary: This tool provides performance reports for Crunch containers.
  • arvados-client: This tool provides subcommands for inspecting Crunch containers, both interactively while they’re running and after they’ve finished.

After Installation: Check your environment

Once you are logged in or have command line tools installed, move on to getting an API token and checking your environment.

Previous: Processing Whole Genome Sequences 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.