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Prerequisites 

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.

Initialisation

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. 

Code Block
titleInstall Catalog
./opencga-admin.sh catalog install --algorithm HS256 --secret-key any_string_you_want -p <<< admin_P@ssword


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.

Code Block
titleCreate User
./opencga-admin.sh users create -p -u test --email test@gel.ac.uk --name "John Doe" --user-password user_P@ssword <<< admin_P@ssword

Now we will use this newly created user "test" for further actions. First, we will need to authenticate as that user: 

Code Block
titleLogin
./opencga.sh users login -u test -p <<< user_P@ssword

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 : 

Code Block
languagexml
titlesession.json
{
  "userId" : "test",
  "token" : "eyJhbGciOiJIUzI1NiJ9.eyJzdWIiOiJ0ZXN0IiwiYXVkIjoiT3BlbkNHQSB1c2VycyIsImlhdCI6MTUxMzAwOTQ2MiwiZXhwIjoxNTEzMDEzMDYyfQ.PAgz4hus2oL4wRCxt2JJ54_jR-efjiERRrFgg49Pkrs",
  "login" : "2017-12-11T15:31:59.616",
  "logout" : null,
  "projectsAndStudies" : { }


Now with new user, we create a project name "Reference studies GRCh37" and alias "reference_grch37" with the following command :

Code Block
titleCreate Project
./opencga.sh projects create -a reference_grch37 -n "Reference studies GRCh37" --organism-scientific-name "Homo sapiens" --organism-assembly "GRCh37"

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"

Code Block
titleCreate Study
./opencga.sh studies create -a 1kG_phase3 -n "1000 Genomes Project - Phase 3" --project reference_grch37


Now, we will create a dummy sample that we'll use to show how to add annotations to.

Code Block
titleCreate sample
./opencga.sh samples create -n sample1 -s 1kG_phase3


Now, we will create a dummy individual that will also contain some annotations:

Code Block
titleCreate individual
./opencga.sh individuals create -n individual1 -s 1kG_phase3


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:

Code Block
languagebash
./opencga.sh variables create --json demo/individual_vs.json -n individual_private_details --confidential --description "Private details of the individual" -s 1kG_phase3 --of yaml
./opencga.sh variables create --json demo/sample_vs.json -n sample_metadata --description "Sample origin" -s 1kG_phase3 --of yaml

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:

Code Block
languagebash
# Annotate the sample sample1 using the variable set 'sample_metadata'
./opencga.sh samples annotation-sets-create --annotation-set-name sampleAnnotName --annotations demo/sample_as.json --id sample1 --variable-set-id sample_metadata
-s 1kG_phase3


# Annotate the individual individual1 using the variable set 'individual_private_details'
./opencga.sh individuals annotation-sets-create --annotation-set-name individualAnnotName --annotations demo/individual_as.json --id individual1 --variable-set-id individual_private_details -s 1kG_phase3


Querying Clinical Data

Querying individuals

Code Block
languagebash
# Querying all individuals annotated with gender = MALE. Result: The only individual we have created
./opencga.sh individuals search --annotation gender=MALE --variable-set individual_private_details

# Querying all individuals annotated with age < 60. Result: None because the individual we annotated has age = 60
./opencga.sh individuals search --annotation "age<60" --variable-set individual_private_details

# But we can obtain it if we change the query to age <= 60 as follows
./opencga.sh individuals search --annotation "age<=60" --variable-set individual_private_details

# Querying all individuals with age <= 60 and gender = FEMALE. No results because our individual is a MALE.
./opencga.sh individuals search --annotation "age<=60;gender=FEMALE" --variable-set individual_private_details

# Now we change the query to age <=60 and gender = MALE. We get again the individual we expected.
./opencga.sh individuals search --annotation "age<=60;gender=MALE" --variable-set individual_private_details


Querying samples

Code Block
languagebash
# Querying all samples annotated with tissue = "umbilical cord blood". Result: The only sample we have created
./opencga.sh samples search --annotation tissue="umbilical cord blood" --variable-set sample_metadata


# Querying all samples annotated with tissue = "umbilical cord blood" and cell type = "multipotent progenitor"
./opencga.sh samples search --annotation "tissue=umbilical cord blood;cell_type=multipotent progenitor" --variable-set sample_metadata


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