A genome "sketch" is a set of preprocessed data that makes it fast to compare genomes and get a similarity score. This is useful for doing genome searches, where you can find a list of similar genomes from a query genome.
This is a KBase dynamic (persistent) service that takes workspace IDs pointing to Assemblies, Genomes, or Reads and returns a list of similar genomes.
Build and run the server locally with:
$ make build
$ make serve
The app's directory will be volume mounted in the container, so you don't have to restart the server to see changes.
With the docker server running on localhost:5000
, run:
$ make test
There are some simple service integration tests located in src/kbase/sketch/test/test_api.py
.
Important files:
kbase.yml
andcompile_report.json
are the main configuration required by KBaseentrypoint.sh
is the docker container's entrypoint script. The option with no arguments runs the python server.Dockerfile
defines our container andrequirements.txt
defines our pip dependencies.- The actual server code lives in
src/kbase/sketch