README.md

Vector Oligo Search

This site provides a database of knockout designs targeting the entire Plasmodium berghei protein encoding genome using the PbHiT CRISPR system as described in Jonsdottir et al. DOI: https://doi.org/10.1101/2024.04.20.590404 Synthetic fragments are ranked by guide RNA scoring.

Generated by the Bushell lab at Umeå University. http://www.bushelllab.com/

Running the development environment

This builds and runs the service using Flask, and mounts the current directory as /app within the containter:

$ docker compose build
$ docker compose up -d

The running service will be avaliable at http://localhost:5000/.

To stop the service:

$ docker compose down

Running the production environment

This builds and runs the service using Gunicorn in a self-contained container:

$ docker build -t crispr:latest .
$ docker run --rm --name crispr --publish 127.0.0.1:5000:5000 -d crispr:latest

The running service will be avaliable at http://localhost:5000/.

To stop the service:

$ docker stop crispr

Alternatively, using docker compose:

$ docker compose -f docker-compose.prod.yml build
$ docker compose -f docker-compose.prod.yml up -d

To stop the service:

$ docker compose down

Using the public image

The image is built from either the main branch or any tag. Tags are created for each release and the tag latest will always point to the same commit as the latest released version.

To use an image you can access it from githubs registry as follows:

docker pull ghcr.io/nbisweden/vector-oligo-search:main