Metadata-Version: 2.1
Name: cirrocumulus
Version: 0.0.5
Summary: scRNA-Seq visualization tool
Home-page: https://github.com/klarman-cell-observatory/cirrocumulus
Author: Joshua Gould
Author-email: jgould@broadinstitute.org
License: UNKNOWN
Description: cirrocumulus
        ===============
        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”
        
        
        .. image:: https://travis-ci.org/klarman-cell-observatory/cirrocumulus.svg?branch=master
            :target: https://travis-ci.org/klarman-cell-observatory/cirrocumulus
        
        .. _Google Cloud SDK: https://cloud.google.com/sdk/install
        .. _App Engine: https://cloud.google.com/appengine/docs/
        .. _Node.js: https://nodejs.org/
Keywords: single cell/nucleus genomics visualization
Platform: UNKNOWN
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Requires-Python: >=3.6
Description-Content-Type: text/x-rst
Provides-Extra: test
