Terra#

Launching Giotto on the Cloud#

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

Setting up your Terra account#

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

Creating a Billing Account#

  • Create an account on the Google Cloud Platform.

  • Set Terra as a billing user on your account.

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

For additional information about billing account go to this link .

Create A Workspace#

  • Create a workspace within your billing account.

Note

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

  • Launch a Virtual Machine with a Cloud environment.

Create a Cloud Environment#

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

Now you can install the Giotto package by running the R commmand:

remotes::install_github('drieslab/Giotto')

Create a ready-to-use Cloud Environment with Giotto#

You can pre-install the Giotto package while launching the Jupyter notebook or the RStudio App.

  • To create a customized Jupyter notebook, use our Terra-based Docker image: giottopackage/terra_jupyter_suite:latest

../../_images/02_docker.png
  • To create a customized RStudio session use the startup script url:gs://fc-c374290b-2c96-4980-8b43-92770eebf1b1/suite.sh

../../_images/03_startup_script.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 on the upper right corner.

  • Select Share option.

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

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

  • Click the save button.

../../_images/04_share.png
Considerations to take into account when sharing with collaborators in Terra
  • Keep in mind that all Cloud environments (virtual machines) launched within the same workspace are linked to the same billing account.

  • Simultaneous modification of notebooks are 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.