Template Pathoplexus Instance

This repo contains a script for reproducing the current Pathoplexus LAPIS, SILO instances locally or in a docker container using the latest LAPIS, SILO versions. The script requires passing the Pathoplexus organism name as an argument, it will create a folder with the configuration required to run SILO, LAPIS.

Before running this script make sure you have built the legacyNdjsonTransformer (found in the tools folder) and have installed yq.

Run the script with:

bash configure.sh <ORGANISM>

It is easiest to run SILO from inside the folder generated by the script:

cd ../../localTestData/ppxData/<ORGANISM>
../../../build/Release/silo preprocessing --database-config database_config.yaml --preprocessing-config preprocessing_config.yaml
../../../build/Release/silo api --api-port 8091

To run SILO and LAPIS in a docker container you can run:

SILO_TAG=latest LAPIS_TAG=main docker compose -f docker_compose.yml up

If you only want to run SILO locally and have LAPIS in a container you can update the docker compose LAPIS instance to use command: "--silo.url=http://host.docker.internal:${SILO_PORT}".

Testing

To test the instance you can send LAPIS queries in the form of:

curl http://localhost:8090/sample/unalignedNucleotideSequences

and SILO queries in the form of:

curl -X POST http://localhost:8091/query \
  -H "Content-Type: application/json" \
  -d '{
      "action": {
        "type": "Fasta",
        "sequenceNames": ["unaligned_main"]
      },
      "filterExpression": {
        "type": "True"
      }
  }'

To test thread-related issues it makes sense to limit the number of requests that can be handled by SILO using --api-threads-for-http-connections when running the SILO api.

Earlier SILO/LAPIS versions

To use a version of SILO older than v0.9.0 use the database_config.old.yaml instead of the database_config.yaml, for versions older than v0.8 additionally use get-released-data.ndjson.zst instead of get-released-data.modified.ndjson.zst.