Citation for coot software how to#
Citation for coot software full#
Citation for coot software software#

A minimal config would consist of SECRET_KEY and MONGO_DBNAME. Most of the config settings are optional.

# enable Phenomizer gene predictions from phenotype terms PHENOMIZER_USERNAME = '?' PHENOMIZER_PASSWORD = '?' # enable Chanjo coverage integration SQLALCHEMY_DATABASE_URI = '?' REPORT_LANGUAGE = 'en' # or 'sv' # other interesting settings SQLALCHEMY_TRACK_MODIFICATIONS = False # this is essential in production TEMPLATES_AUTO_RELOAD = False # consider turning off in production SECRET_KEY = 'secret key' # override in production! # scoutconfig.py # list of email addresses to send errors to in production ADMINS = [ = 'localhost' MONGO_PORT = 27017 MONGO_DBNAME = 'scout' MONGO_USERNAME = 'testUser' MONGO_PASSWORD = 'testPass' # enable user authentication using Google OAuth 2.0 GOOGLE = dict(Д¬lient_id = 'client_id_', Including user authentication, coverage, and local observations. Information you provide you activate different parts of the interface automatically, Scout needs a server config to know which databases to connect to etc. Scout may be configured to link to a local Gens installation. Integration with Gens for displaying copy number profiles for variants

Citation for coot software how to#

Instructions on how to enable this feature can be found in the document Scout may be configured to visualize local variant frequencies monitored by Loqusdb. Integration with loqusdb for integrating local variant frequencies How to enable this feature can be found in the document chanjo_coverage_integration. Scout may be configured to visualize coverage reports produced by Chanjo. Scout load case scout/demo/ Integration with chanjo for coverage report visualization Instructions on how to run a Scout image connected to your local database or a custom database are present on this page. Once the server has started you and open the app in the web browser at the following address: The command to stop the demo are either docker-compose down or make down.

scout-web -> the Scout web app, that serves the app on localhost, port 8000.

scout-cli -> the Scout command line, connected to the database.

a MongoDB instance, on the default port 27017 in the container, mapped to host port 27013.

Citation for coot software full#

To see a full list and description of these shortcuts run: make help. The repository includes a Makefile with common shortcuts to simplify setting up and working with Scout.

Citation for coot software software#

Runnable demo image - does not require installing of software and databaseДЄ simple demo instance of Scout requires the installation of Docker and can be launched either by using the command: This README only gives a brief overview of Scout, for a more complete reference, please check out our docs. Collaboration - Write comments and share cases between users and institutes.Aggregation - Combine results from multiple analyses and VCFs into a centralized database.Simple - Analyze variants in a simple to use web interface.Analyze VCFs and collaborate on solving rare diseases quicker