KBase Genome 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.

Usage

Basic requests

From the terminal, you can use the curl command to access the sketch service. Since the sketch serivce is a KBase dynamic service, you will have to find its active URL by searching for it here: "https://ci.kbase.us/#catalog/services".

The service accepts POST requests with a JSON payload with the following parameters:

{
  "params": {
    "ws_ref": <workspace reference>
    "n_max_results": <integer between 1 and 100 (optional)>
    "bypass_caching": <boolean (optional)>
  }
}

Development

Set up the environment

You can use the following env vars:

• KBASE_ENDPOINT - required - eg "https://ci.kbase.us/services/"
• KBASE_SECURE_CONFIG_PARAM_service_token - required - a KBase auth token that represents this service, used for making requests to the caching service
• KBASE_SECURE_CONFIG_PARAM_CACHING_SERVICE_URL - optional
• KBASE_SECURE_CONFIG_PARAM_HOMOLOGY_URL - optional - defaults to https://homology.kbase.us
• KBASE_SECURE_CONFIG_PARAM_ID_MAPPER_URL - optional - defaults to use KBASE_ENDPOINT with /idmapper/api/v1
• KBASE_SECURE_CONFIG_PARAM_HOMOLOGY_NAMESPACE - optional - defaults to NCBI_Refseq

Running and testing

Build and run locally with:

$ docker-compose up

Run tests with docker-compose run web test in a separate terminal window

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/server.py