From 3d3f2bbde0cb2ad15bc3e17ee6d510c6298f1678 Mon Sep 17 00:00:00 2001
From: bot-ross <98030736+bot-ross[bot]@users.noreply.github.com>
Date: Thu, 12 Dec 2024 15:11:31 +0000
Subject: [PATCH] chore: render README.md
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+## Containers
+
+Collection of bioinformatics containers
+
+
+
+
+
+
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+
+
+## Credits
+
+The CI/CD and format of this repository was adapted from onedr0p's [containers](https://github.com/onedr0p/containers). From onedr0p: A lot of inspiration and ideas are thanks to the hard work of [hotio.dev](https://hotio.dev/) and [linuxserver.io](https://www.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](https://fleet.linuxserver.io/) or [Bitnami](https://bitnami.com/stacks/containers).
+
+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](https://github.com/renovatebot/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
+
+```yaml
+networks:
+ boltz:
+ name: boltz
+ external: true
+services:
+ boltz:
+ image: ghcr.io/RareCompute/boltz:1.0.0
+ container_name: boltz
+ user: 65534:65534
+ # ...
+```
+
+### Kubernetes
+
+```yaml
+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](https://kubernetes.io/docs/tasks/inject-data-application/define-command-argument-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.
+
+ ```yaml
+ 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](https://github.com/RareCompute/containers/pkgs/container/boltz) | stable | ghcr.io/RareCompute/boltz
+[chai](https://github.com/RareCompute/containers/pkgs/container/chai) | stable | ghcr.io/RareCompute/chai
+[chai-amelie](https://github.com/RareCompute/containers/pkgs/container/chai-amelie) | stable | ghcr.io/RareCompute/chai-amelie
+[devserver](https://github.com/RareCompute/containers/pkgs/container/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.
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