HGVA CLI is powered by the Open Computational Genomic Analysis (OpenCGA) project and makes intensive use of the HGVA's RESTful Web services. OpenCGA CLI implements an extensive API that enables numerous operations over metadata, samples and genomic data. We will here focus on those commands of the API which are of more interest for HGVA users, giving examples of their use and pin pointing certain peculiarities of the parameters for HGVA.

Installation

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 https://github.com/opencb/opencga.git

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

https://github.com/opencb/opencga/releases

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

https://github.com/opencb/opencga

The CLI interface is accessible through the opencga.sh script:

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

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

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

Commands:
         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

Configuration

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 "http://bioinfodev.hpc.cam.ac.uk/hgva-1.0":

---
## number of seconds that session remain open
sessionDuration: 12000

## REST client configuration options
rest:
  host: "http://bioinfodev.hpc.cam.ac.uk/hgva-1.0"
  batchQuerySize: 200
  timeout: 10000
  defaultLimit: 2000

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

General usage

The CLI provides commands, subcommands and parameters to access its functionality. Commands of most interest for HGVA users are projects, studies and samples. Please, refer The CLI is implemented by JCommander and organises its functionality by using commands, subcommands and parameters. Please, srefer to the tutorial Using the Command Line for further information.