Terra#

Launching Giotto on the Cloud#

You can run all your pipelines using Giotto on the Cloud through the Terra platform.

Setting up your Terra account#

Go to Terra on the Chrome browser and Sign Up using the same email address that you will use for the Google Cloud billing account.

Creating a Billing Account#

  • Create an account on the Google Cloud Platform. You can start a free trial with a $300 credit.

  • Set Terra as a billing user on your Google account by following these steps.

  • Select your Google account to create a billing project on Terra.

For additional information about billing accounts go to this link .

Create A Workspace#

  • Create a workspace under your billing account.

Note

All users with access permissions to your workspace will share the same billing account.

  • You can upload your own data or download data from public databases to the workspace.

  • Launch a Cloud environment or Virtual Machine to start the analysis.

Create a Cloud Environment#

In Terra, you can run Cloud Environments using Jupyter notebooks or the RStudio App. We recommend using the Juypyter notebook + Python + Bioconductor or the RStudio + Bioconductor options.

../../_images/01_environments.png

You can customize the memory usage, the number of CPUs, and the persistent disk size for your virtual machine.

../../_images/01_vm.png

Once you launched either a Jupyter notebook or the RStudio App, you can install the Giotto package:

## Install the master branch
remotes::install_github("drieslab/Giotto")

## Install the suite branch
remotes::install_github("drieslab/Giotto@suite")

If you prefer to launch a Juptyter notebook ready to run analysis with Giotto, you can use our Terra-based Docker image for the master or suite branch.

You can also launch the RStudio app using the Giotto’s startup script for the master or suite branch.

Customizing your Cloud Environment using Giotto’s Docker image#

Under Application configuration, use the option Custom Environment and introduce the link to the Docker container, named josschavezf/terra-jupyter-bioconductor-giotto:latest or josschavezf/terra-jupyter-python-bioconductor-giotto_suite:latest

../../_images/02_docker.png

Customizing your Cloud Environment using a Startup Script#

You can download the Startup Script from this link .

  • Upload the Startup Script to your Workspace Files.

../../_images/03_upload.png

  • Click on the startup_script.sh document and copy the gs link.

../../_images/03_view.png

  • Copy and paste the link under the Startup Script option to launch the Cloud environment.

../../_images/03_cloud.png

  • Click on Create Environment

Share your workspace with collaborators#

You can share your workspace with collaborators, including data, notebooks, and workflows stored in your workspace.

  • Go to the Dashboard tab on your workspace and click the three dots in the upper right corner.

  • Select the Share option.

  • Add the email of your collaborator. They will receive an invitation for joining the workspace.

  • You can select the permissions granted to your collaborator (reader, writer, or owner).

  • Click the save button.

../../_images/04_share.png
Considerations when collaborating in Terra

  • All Cloud environments (virtual machines) launched within the same workspace are linked to the same billing account.

  • Simultaneous modification of notebooks is not allowed.

  • Opening the notebook while someone else is editing will show a message, but the current editor is not notified when someone else is trying to open the notebook.