seqcolapi

This repository contains:

1. Sequence collections API software (the seqcolapi package). This package is based on the refget package. It simply provides an wrapper to implement the Sequence Collections API.
2. Configuration and GitHub Actions for demo server instance (servers subfolder).

Instructions

Run locally for development

To run a local server with a local database:

source servers/localhost/dev_local.env
uvicorn seqcolapi.main:app --reload --port 8100

To run a local server with the production database:

source servers/seqcolapi.databio.org/production.env
uvicorn seqcolapi.main:app --reload --port 8100

Running with docker

To build the docker file:

docker build --no-cache -t scim .

To run in a container:

export POSTGRES_PASSWORD=`pass aws/rds_postgres` 
docker run --rm -p 8000:8000 --name sccon \
  --env "POSTGRES_PASSWORD" \
  --volume $CODE/seqcolapi.databio.org/config/seqcolapi.yaml:/config.yaml \
  scim seqcolapi serve -c /config.yaml -p 8000

To deploy container to dockerhub:

Use github action in this repo which deploys on release, or through manual dispatch.

Left to do:

• it already retrieves from a refget server.
• let me insert stuff using only checksums.
• make it take 2 refget servers correctly.

To load new data into seqcolapi.databio.org

cd analysis
source ../servers/localhost/dev_local.env
ipython3

Now run load_fasta.py

Deploy to AWS ECS

Testing locally first

Build the seqcolapi image

cd
docker build -t docker.io/databio/seqcolapi:latest .

docker pull docker.io/databio/seqcolapi:latest
cd servers/seqcolapi.databio.org
docker build -t scim .
docker run \
  -e POSTGRES_HOST=$POSTGRES_HOST \
  -e POSTGRES_PASSWORD=$POSTGRES_PASSWORD \
  --network=host \
  scim

Deploying

To upgrade the software:

Use config file located in /servers/seqcolapi.databio.org. This will use the image in docker.io://databio/seqcolapi, github repo: refgenie/seqcolapi as base, bundle it with the above config, and deploy to the shefflab ECS.

1. Ensure the refget package master branch is as you want it.
2. Deploy the updated secqolapi app to dockerhub (using manual dispatch, or deploy on github release).
3. Finally, deploy the instance with manual dispatch using the included GitHub action.