cirrocumulus 0.0.3.post2

scRNA-Seq visualization tool

Interactive single cell visualization application.

• Run on Google App Engine or your desktop

• Scales to > 6 million cells on commodity hardware

• Share datasets with collaborators

• Interactively create and share cell annotations

• Explore multiple features and embeddings simultaneously

• Visualize 3-d embeddings

Local Usage

• Install using pip:

  pip install cirrocumulus

• Launch via the command line:

  cirro launch <path to dataset>

Google Cloud Platform (GCP) Deployment Instructions

• Clone the cirrocumulus repository:

  git clone https://github.com/klarman-cell-observatory/cirrocumulus

• Change your current working directory to cirrocumulus:

  cd cirrocumulus

• Install Node.js.

• Install JavaScript dependencies:

  npm i

• Build the client:

  npm run-script build

• Create or use an existing GCP project

• Create an OAuth client id

  • In Google Console, navigate to APIs and Services > OAuth consent screen. Set the OAuth consent screen application name and add <PROJECT>.appspot.com to the list of “Authorized domains”

  • Go to Credentials and click “Create Credentials > OAuth client ID”. Enter “Web application” for “Application Type” and https://<PROJECT>.appspot.com for “Authorized JavaScript origins”. Click “Create” to create the credentials.

  • Copy OAuth client id into cirrocumulus/cirro/config.json.

• Create App Engine by navigating to App Engine > Dashboard. You may choose the region where your application is hosted. Select the Python 3 Standard Environment.

• Install the Google Cloud SDK. Type gcloud init in your terminal if this is your first time using the Google Cloud SDK.

• Deploy the application using the command below. Remember to replace <PROJECT> with your project ID.:

  gcloud app deploy app.yaml --project=<PROJECT>

  Your project is available at https://<PROJECT>.appspot.com.

• Go to https://<PROJECT>.appspot.com in your web browser and login.

  • By default, no one is allowed to add datasets to your application.

  • In Google Console, navigate to Data Store > Entities and click on your email address. Add the property importer of type boolean and set it to true.

  • Go back to https://<PROJECT>.appspot.com and start adding datasets.

• Read more about App Engine, such as how you can limit spending.

Developer Instructions

• Install JavaScript dependencies:

  npm i

• Build the client:

  npm run-script build

• Install Python module in editable mode:

  pip install -r requirements.txt -e .

• Add http://localhost:5000 to your Web application Outh client ID authorized JavaScript origins at APIs and Services > Credentials

• Download the App Engine service account JSON key from IAM & admin > Service accounts (DO NOT SHARE THIS!) and set the environment variable GOOGLE_APPLICATION_CREDENTIALS:

  export GOOGLE_APPLICATION_CREDENTIALS=“/home/user/Downloads/service-account-file.json”