jayrbolton / sketch_service

Service that returns similar genomes from a given assembly/genome ID

KBase Sketch Service

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.

Development

Running the server

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.

Testing

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.

Project anatomy

Important files:

• kbase.yml and compile_report.json are the main configuration required by KBase
• entrypoint.sh is the docker container's entrypoint script. The option with no arguments runs the python server.
• Dockerfile defines our container and requirements.txt defines our pip dependencies.
• The actual server code lives in src/kbase/sketch