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.
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.
You can customize the memory usage, the number of CPUs, and the persistent disk size for your virtual machine.
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
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.
Click on the startup_script.sh document and copy the gs link.
Copy and paste the link under the Startup Script option to launch the Cloud environment.
Click on Create Environment