A working setup of openCGA is required to setup a Testing environment. If user hasn't yet set it up, please follow the steps on installation guide and set it up.
All of the following steps assume, user is under openCGA installation directory (/opt/opencga/).
The following CLI command will create the database, the collections and all the indexes, it also creates the admin user with the specified password. The MongoDB database host and name are read from the /conf/catalog-configuration.yml file by default.
This following command will create a user name "John Doe" and ID "test". Note that as by default OpenCGA is configured as private, only the OpenCGA admin user can create other users. We are using opencga-admin CLI.
Now we will use this newly created user "test" for further actions. First, we will need to authenticate as that user:
This will create a hidden directory in your home called .opencga. This directory will contain a file named ~/.opencga/session.json with the user id and the valid token. This will be used automatically by opencga.sh and will only be valid for some minutes, by doing this users do not have to write the password too many times. The contents of session.json file will look like :
Now with new user, we create a project name "Reference studies GRCh37" and alias "reference_grch37" with the following command :
Note: organism-scientific-name and organism-assembly should be available in CellBase. User can get this information using the following public WS: http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/meta/species
Next step, create a study name "" inside project "reference_grch37"
Now, we will create a dummy sample that we'll use to show how to add annotations to.
Now, we will create a dummy individual that will also contain some annotations:
Ingesting Clinical Data (creating Variable Sets and Annotation Sets)
We are going to use the Variable Sets and Annotation Sets used in the examples of the Clinical Data section. Here are the files needed to load those Variable Sets and Annotation Sets using the command line: demo.tar.gz
First, we will need to load both Variable Sets. To do so, we will run the following command lines:
From that moment on, we can annotate using any of the Variable Sets any of the Annotable entries. For example, to annotate both the sample and the individual we created we will run the following commands:
Querying Clinical Data
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