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.
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
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
}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
See the LICENSE
Please raise any issues on Github