Skip to main content
Join the official 2019 Python Developers SurveyStart the survey!

scRNA-Seq visualization tool

Project description

Interactive single cell visualization in the cloud or on your desktop.

Local Usage

  • Install using pip:

    pip install cirrocumulus
    
  • Launch via the command line:

    cirro <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”
    

Project details


Release history Release notifications

This version

0.0.2

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for cirrocumulus, version 0.0.2
Filename, size File type Python version Upload date Hashes
Filename, size cirrocumulus-0.0.2-py3-none-any.whl (25.1 kB) File type Wheel Python version py3 Upload date Hashes View hashes
Filename, size cirrocumulus-0.0.2.tar.gz (194.0 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page