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The CLI is distributed with the rest of the OpenCGA code. The OpenCGA code can be cloned in your machine by executing in your terminal:

$ git clone

Alternatively, you can download tar.gz files with the code for the latest tags/releases of OpenCGA from:

Once you have downloaded the code, follow the instructions at the How to Build section of the OpenCGA repository:

The CLI interface is accessible through the script:

$ cd opencga
opencga$ cd build
opencga/build$ cd bin
opencga/build/bin$ ./

Program:     OpenCGA (OpenCB)
Version:     0.9.0-dev
Git commit:  a1ab0decf97556241b446d23cc596ecb5a3f997c
Description: Big Data platform for processing and analysing NGS data

Usage: [-h|--help] [--version] <command> [options]

         users  User commands
      projects  Project commands
       studies  Study commands
         files  Files commands
          jobs  Jobs commands
   individuals  Individuals commands
       samples  Samples commands
     variables  Variable set commands
       cohorts  Cohorts commands
         tools  Tools commands
        panels  Panels commands


As previously said, the CLI makes intensive use of the RESTful API. Thus, the only configuration detail needed for the CLI to work is a URL where the Web Services API is hosted. The configuration file client-configuration.yml is used for this purpose. You shall find a template of this file at the build/conf directory:

$ ll opencga/build/conf/client-configuration.yml
-rw-r--r-- 1 fjlopez fjlopez 290 Oct 24 17:49 opencga/build/conf/client-configuration.yml

Edit this file with any text editor and set the rest → host attribute to "":

Configuration file client-configuration.yml
## number of seconds that session remain open
sessionDuration: 12000

## REST client configuration options
  host: ""
  batchQuerySize: 200
  timeout: 10000
  defaultLimit: 2000

## gRPC configuration options
  host: "localhost:9091"


The CLI provides commands, subcommands and parameters to access its functionality. Commands of most interest for HGVA users are projectsstudies and samples. Please, find below a list of commands which can be of most interest for HGVA user.

Getting information about genomic variants

Getting variant data from a given study:{project}:{study}

An extensive list of filtering parameters allow great flexibility on the queries (check Swagger documentation link above). For example, get TTN variants from the Genome of the Netherlands study, which is framed within the reference_grch37 project. We will also limit the number of returned results to 3:

Getting information about projects

Getting all metadata from a particular project:{projects}/info

For example, getting all metadata for the reference_grch37 project:

Getting all metadata from all studies associated to a particular project:{projects}/studies

For example, getting all studies and their metadata for the cancer_grch37 project:

Getting information about studies

Get all available studies and their metadata. Please note, of special interest will be here the field alias which contains the study identifier to be used as an input whenever a study must be passed as a parameter:

For example, getting all metadata for all available studies:

Getting summary data from a particular study:{project}:{study}/summary

For example, getting summary data for study 1kG_phase3 which is framed within project reference_grch37:

Getting all available metadata for a particular study:{project}:{study}/info

For example, getting all metadata for study GONL  which is framed within the project reference_grch37:

Getting all samples metadata for a given study:{project}:{study}/samples

For example, getting all samples metadata for study 1kG_phase3 which is framed within project reference_grch37. Please, note that not all studies contain samples data, e.g. GONL, ExAC, among others, only provide variant lists and aggregated frequencies, i.e. no sample genotypes.

Getting information about samples

Get all metadata for a particular sample:{sample}/info?study={project}:{study}

For example, get all metadata for sample HG00096 of the 1kG_phase3 study which is framed within the reference_grch37 project:

Getting information about cohorts

Getting all samples metadata in a given cohort:{cohort}/samples?study={project}:{study}

For example, get all samples metadata for cohort GBR from study 1kG_phase3 which is framed within project reference_grch37:

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