{"id":27786,"library":"ga4gh","title":"GA4GH Server","description":"A reference implementation of the Global Alliance for Genomics and Health (GA4GH) API for genomic data. Versions 0.3.x are alpha pre-releases with major breaking changes (protobuf migration, modularization, package rename). As of v0.3.6 the package is renamed to ga4gh-server on PyPI.","status":"active","version":"0.3.5","language":"python","source_language":"en","source_url":"https://github.com/ga4gh/server","tags":["genomics","bioinformatics","GA4GH","API","reference-implementation"],"install":[{"cmd":"pip install ga4gh==0.3.5","lang":"bash","label":"Legacy package"},{"cmd":"pip install ga4gh-server","lang":"bash","label":"Current package (>=0.3.6)"}],"dependencies":[{"reason":"Protocol Buffers gRPC support","package":"grpcio","optional":false},{"reason":"Protocol Buffers serialization","package":"protobuf","optional":false},{"reason":"Web server framework","package":"flask","optional":false}],"imports":[{"note":"Old import path removed in v0.3.5 due to modularization","wrong":"from ga4gh.frontend import FlaskGA4GHApplication","symbol":"FlaskGA4GHApplication","correct":"from ga4gh.server.frontend import FlaskGA4GHApplication"},{"note":"CLI moved to ga4gh.server.cli in v0.3.4","wrong":"from ga4gh.cli import configure","symbol":"configure","correct":"from ga4gh.server.cli import configure"}],"quickstart":{"code":"from ga4gh.server.frontend import FlaskGA4GHApplication\nfrom ga4gh.server.cli import configure\nimport os\n\napp = FlaskGA4GHApplication()\nconfig = os.environ.get('GA4GH_CONFIG', 'config.py')\nconfigure(app, config) \napp.run()","lang":"python","description":"Initialize GA4GH server with Flask. Set GA4GH_CONFIG environment variable to point to your configuration file."},"warnings":[{"fix":"pip uninstall ga4gh; pip install ga4gh-server","message":"Package renamed from 'ga4gh' to 'ga4gh-server' starting from v0.3.6. All future versions will be published as ga4gh-server. Install the new package for updates.","severity":"breaking","affected_versions":">=0.3.6"},{"fix":"Re-export data to Protobuf format; update clients to use protobuf instead of avro.","message":"In v0.3.1, the serialization format switched from Avro to Protocol Buffers. Existing data files and client applications are incompatible.","severity":"breaking","affected_versions":">=0.3.1"},{"fix":"Change imports to 'from ga4gh.server.frontend' etc.","message":"In v0.3.5, the package was modularized into ga4gh, ga4gh-schemas, ga4gh-client, ga4gh-common. Import paths changed; old imports 'from ga4gh.frontend' no longer work.","severity":"breaking","affected_versions":">=0.3.5"},{"fix":"Install ga4gh-client for client API.","message":"The 'ga4gh' package on PyPI is the server package, not a client library. For client functionality, use 'ga4gh-client' (pip install ga4gh-client).","severity":"gotcha","affected_versions":">=0.3.5"}],"env_vars":null,"last_verified":"2026-05-09T00:00:00.000Z","next_check":"2026-08-07T00:00:00.000Z","problems":[{"fix":"Use 'from ga4gh.server.frontend import FlaskGA4GHApplication'","cause":"Module structure changed in v0.3.5; frontend code moved under ga4gh.server.","error":"ImportError: No module named 'ga4gh.frontend'"},{"fix":"Run 'pip install ga4gh-server' instead of 'pip install ga4gh'","cause":"Package renaming to 'ga4gh-server' in v0.3.6; attempting to install 'ga4gh' no longer exists for newer versions.","error":"ModuleNotFoundError: No module named 'ga4gh'"},{"fix":"Install 'pip install ga4gh-schemas' and import from 'ga4gh.schemas'","cause":"Schemas extracted to separate package 'ga4gh-schemas' in v0.3.5.","error":"AttributeError: module 'ga4gh' has no attribute 'schemas'"}],"ecosystem":"pypi","meta_description":null,"install_score":null,"install_tag":null,"quickstart_score":null,"quickstart_tag":null}