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License Coverage Status Python 3.6

htsget Compliance

The htsget Compliance Suite determines a web service's compliance with the htsget API specification for serving large alignment and variant datasets. The specification, developed by the Global Alliance for Genomics and Health, serves to provide a standardized, interoperable API framework across different institutions.

Installation

To install, clone the Github repository, then install via setuptools:

git clone https://github.com/ga4gh/htsget-compliance.git
cd htsget-compliance
python setup.py install

Quickstart

Running the following:

% htsget-compliance https://htsget.ga4gh-demo.org  | jq '.["summary"]'

Should ideally yield:

{
  "run": 12,
  "passed": 12,
  "warned": 0,
  "failed": 0,
  "skipped": 0
}

Usage

The compliance tests can be run via htsget-compliance ${HTSGET_URL}, where HTSGET_URL is the base url to an htsget service. For example:

htsget-compliance https://htsget.ga4gh-demo.org

Additional commandline options can be specified to:

  • write JSON report to file (-f)
  • change the url path to alignment objects from the default /reads/{id} (-r)
  • change the url path to variant objects from the default /variants/{id} (-v)
  • etc.

A full list of options can be displayed via htsget-compliance --help

Requires Samtools suite to be available in your path

License

See the LICENSE

Issues

Please raise any issues on Github