Containers

Collection of bioinformatics containers

Credits

The CI/CD and format of this repository was adapted from onedr0p's containers. From onedr0p: A lot of inspiration and ideas are thanks to the hard work of hotio.dev and linuxserver.io contributors.

Tag immutability

The containers built here do not use immutable tags, as least not in the more common way you have seen from linuxserver.io or Bitnami.

We do take a similar approach but instead of appending a -ls69 or -r420 prefix to the tag we instead insist on pinning to the sha256 digest of the image, while this is not as pretty it is just as functional in making the images immutable.

Container	Immutable
ghcr.io/RareCompute/boltz:rolling	❌
ghcr.io/RareCompute/boltz:1.0.0	❌
ghcr.io/RareCompute/boltz:rolling@sha256:...	✅
ghcr.io/RareCompute/boltz:1.0.0@sha256:...	✅

If pinning an image to the sha256 digest, tools like Renovate support updating the container on a digest or application version change.

Rootless

To run these containers as non-root make sure you update your configuration to the user and group you want.

Docker compose

networks:
  boltz:
    name: boltz
    external: true
services:
  boltz:
    image: ghcr.io/RareCompute/boltz:1.0.0
    container_name: boltz
    user: 65534:65534
    # ...

Kubernetes

apiVersion: apps/v1
kind: Deployment
metadata:
  name: boltz
# ...
spec:
  # ...
  template:
    # ...
    spec:
      # ...
      securityContext:
        runAsUser: 65534
        runAsGroup: 65534
        fsGroup: 65534
        fsGroupChangePolicy: OnRootMismatch
# ...

Passing arguments to an application

Some applications do not support defining configuration via environment variables and instead only allow certain config to be set in the command line arguments for the app. To circumvent this, for applications that have an entrypoint.sh read below.

1. First read the Kubernetes docs on defining command and arguments for a Container.

2. Look up the documentation for the application and find a argument you would like to set.

3. Set the extra arguments in the args section like below.

   args:
     - --port
     - "8080"

Configuration volume

For applications that need to have persistent configuration data the config volume is hardcoded to /config inside the container. This is not able to be changed in most cases.

Available Images

Each Image will be built with a rolling tag, along with tags specific to it's version. Available Images Below

Container	Channel	Image
boltz	stable	ghcr.io/RareCompute/boltz
chai	stable	ghcr.io/RareCompute/chai
chai-amelie	stable	ghcr.io/RareCompute/chai-amelie
devserver	stable	ghcr.io/RareCompute/devserver

Deprecations

Containers here can be deprecated at any point, this could be for any reason described below.

1. The upstream application is no longer actively developed
2. The upstream application has an official upstream container that follows closely to the mission statement described here
3. The upstream application has been replaced with a better alternative
4. The maintenance burden of keeping the container here is too bothersome

Note: Deprecated containers will remained published to this repo for 6 months after which they will be pruned.