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Last pushed: 6 months ago
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opencga v1.0.0 final
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opencga v1.0.0 final running on ubuntu 14.04.

Running OpenCGA

Start mongo:

docker run -p 83:27017 -v <LOCATION_OF_YOUR_DATA>:/data/db --name opencgamongo -dit mongo --httpinterface --rest

Start opencga linked to mongo:

docker run --link=opencgamongo:mongo -p 82:8080 -dit sdgsbinfx/opencga:latest /tmp/opencga/docker_startup.sh

Because the IP of the mongo container will not be static you must start the opencga container with docker_startup.sh which will build and configure opencga based on the mongo IP address. It rebuild opencga with these settings, redeploys the webservices and starts tomcat.

New Installations

If this is a new installation login to your container and you need to add an admin password:

/tmp/opencga/build/bin/opencga-admin.sh catalog install -p

You can now add a user - you will be prompted for the admin password.

/tmp/opencga/build/bin/opencga-admin.sh users create --email <EMAIL> -u <USER_ID> --name "<USER_NAME>" --user-password <PASSWORD> -p

You can now use the webservices located at http://localhost:82/opencga-1.0.0-final and mongo is accessible on http://localhost:83

Previously Created

If you already have a catalogdb set up in your data directory then you don't need to create users again.

This is not endorsed by the creators of opencga.

Notes

If you have nested models then you might need to execute this command from within mongodb

db.getSiblingDB('admin').runCommand( { setParameter: 1, failIndexKeyTooLong: false } )

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sdgsbinfx

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