Chapter 2 The AnVIL – workspaces, runtimes, buckets, workflows

In this section we learn about

  • Cloning a ‘WORKSPACES’ for coordinating access to particular data sets and analyses
  • Creating a Notebook runtimes for cloud-based computation
  • Understanding the relationship between workspaace, runtime, DATA, and NOTEBOOKS.

2.2 Use an existing workspace

Visit the WORKSPACES page https://anvil.terra.bio/#workspaces

Search for the ‘Bioconductor’ featured workspace.

  • Choose the HAMBURGER menu, ‘Your workspaces’ item
  • Search (at the top of the screen) for ‘Bioconductor-BCC2020’
  • This should appear under ‘My Workspaces’

  • Problems?

    • Refresh your browser window & cache, with, e.g., command-shift-R
    • Provide your email account to Lori or Nitesh in REMO chat

  • Shortcut: https://anvil.terra.bio/#workspaces?filter=Bioconductor-BCC2020

Clone

  • Choose the TEARDROP associated with this workspace
  • Select ‘Clone’
  • Name the workspace, e.g,. Bioconductor-bcc2020-<YOUR-NAME> or similar.
  • Associate the cloned workspace with the bioconductor-rpci-bcc2020 billing account

2.3 DASHBOARD

Runtimes (top right)

  • Select the ‘R / Bioconductor…’ runtime environment

    • ‘What’s installed on this environment’
    • Compute power

  • Runtime can be used across different workspaces

Google bucket

  • Associated with the work space, managed by Terra. Persistent storage.

2.4 DATA

TABLES

  • Usually, metadata referencing cloud-based data sets
  • Ours: Human Cell Atlas BAM files for a particular study

…

OTHER DATA

  • Google bucket content
  • Persits even if new runtime selected

2.5 NOTEBOOKS

Existing notebooks – TEARDROP

  • Preview: read-only
  • Edit: edit, evaluate, and save changes
  • Playground: edit, evalaute, but do not save changes

2.6 WORKFLOWS