Installation

As described in the documentation, HGVA backend is powered by the OpenCGA project. 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. Checkout the latest code (release-1.1.0 branch):

$ git clone https://github.com/opencb/opencga.git
$ git checkout v1.3.6

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:     01.91.0-dev
Git commit:  a1ab0decf97556241b446d23cc596ecb5a3f997cf2dace56fcdf491efee8ebb0cb43f981e31c320e
Description: Big Data platform for processing and analysing NGS data

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

Catalog Commandscommands:
         users  User commands
      projects  Project commands
       studies  Study commands
         files  FilesFile commands
          jobs  Jobs commands
   individuals  IndividualsIndividual commands
      families  Family commands
       samples  Samples commands
     variables  Variable set commands
       cohorts  Cohorts commands

Analysis commands:
    alignments  Implement several tools for the Toolsgenomic commandsalignment analysis
       panelsvariant  PanelsVariant commands

The CLI provides commands, subcommands and parameters to access its functionality. Commands of most interest for HGVA users are projects, studies, cohorts and samples. Please, find below a list of commands which can be of most interest for HGVA user. Further documentation on the OpenCGA CLI can be found at the Command Lines section of the OpenCGA documentation.

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://bioinfodevbioinfo.hpc.cam.ac.uk/hgva-1.0":

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

## REST client configuration options
rest:
  host: "http://bioinfodevbioinfo.hpc.cam.ac.uk/hgva-1.0"
  batchQuerySize: 200
  timeout: 1000030000
  defaultLimit: 2000

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

Examples

Getting information about

variants

Getting variant data from a given study:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/analysis/variant/query?studies={project}:{study}

You can query variants by using the variant command and query subcommand. An extensive list of filtering parameters allow great flexibility on the queries (check Swagger documentation link above). Please, check inline help provided by opencga.sh for further details. For example, get TTN variants from the Genome of the Netherlands study, which is framed within the reference_grch37 project. We will restrict studies data to those corresponding to GONL. Finally, we will also limit the number of returned results to 3:http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/analysis/variant/query?gene=TTN&studies=GONL&limit=3

./opencga.sh variant query --gene TTN --study GONL --limit 3 --of json --output-study GONL

Getting information about projects

Getting You can use the command projects to query projects data.

For getting all metadata from a particular project :

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/projects/{projects}/info

you can use the info subcommand. For example, getting all metadata for the referencecancer_grch37 project:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/projects/reference_grch37/info

Getting grch37 project:

./opencga.sh projects info --project cancer_grch37

For getting all metadata from all studies associated to a particular project :

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/projects/{projects}/studies

yo ucan use the studies subcommand. For example, getting all studies and their metadata for the cancer_grch37 project:http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/projects/cancer_grch37/studies

./opencga.sh projects studies --project cancer_grch37

Getting information about studies

Get You can use the command studies to query studies data.

For getting all available studies and their metadata . Please you can use the search subcommand. For example, getting all metadata for all available studies (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):

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/search

For example, getting all metadata for all available studies:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/search

./opencga.sh studies search

For getting summary data from a particular study :

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/{project}:{study}/summary

you can use the summary subcommand. For example, getting summary data for study 1kG_phase3 which is framed within project reference_grch37:http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/

./opencga.sh studies summary --study reference_grch37:1kG_phase3

Getting For getting all available metadata for a particular study :

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/{project}:{study}/info

you can use the info command. For example, getting all metadata for study GONL  which is framed within the project reference_grch37:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/reference_grch37:GONL/info

Getting

./opencga.sh studies info --study GONL

For getting all samples metadata for a given study :

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/{project}:{study}/samples

you can use the samples subcommand. 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.http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/

./opencga.sh studies samples --study reference_grch37:1kG_phase3

Getting information about samples

You can use the command samples to query samples data.

Get For getting all metadata for a particular sample :

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/samples/{sample}/info?study={project}:{study}

you can use the info subcommand. For example, get all metadata for sample HG00096 of the 1kG_phase3 study which is framed within the reference_grch37 project:http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/samples/HG00096/info?study=

./opencga.sh samples info --sample HG00096 --study reference_grch37:1kG_phase3

Getting information about cohorts

You can use the cohorts command to query cohorts data.

Getting For getting all samples metadata in a given cohort :

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/cohorts/{cohort}/samples?study={project}:{study}

For you can use the samples subcommand. For example, get all samples metadata for cohort GBR from study 1kG_phase3 which is framed within project reference_grch37:http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/cohorts/GBR/samples?study=

./opencga.sh cohorts samples --study reference_grch37:1kG_phase3 --cohort GBR