Singularity HPC Registry

This is testing having a remote registry for Singularity HPC to use.

under development

📖️ Read the documentation 📖️ ⭐️ Browse the container module collection ⭐️

Contribution

This registry showcases Singularity HPC (shpc), and provides the default set of containers for its default registry. Contributions are very much welcome, so please do submit a pull-request if you'd like more software to be added, or open an issue to request a new addition!

The documentation has an introduction about registries, and explains how to organize the required files for a container entry.

Automated generation

First of all, there is an automated way of getting most of the container.yaml written via GitHub magic 🎩 automation.

Fork of this repository.
Go to the Actions tab.
Select "Generate New Container" in the left-hand side menu.
Click the "Run workflow" dropdown on the right-hand side.
Fill in the name of the container you want to build a container.yaml for, as well as a URL and a description (both are mandatory fields). Leave the branch as main.
Hit the green "Run workflow" button, wait and marvel at the magic ✨ happening. The GitHub Action will automatically open a pull request with most of the container.yaml filled in for you. You can check the branch out, edit it further – in particular refine the list aliases.

BioContainers

We have a script that will generate (non existing) modules for BioContainers, currently under development but will be added to automation soon! To run, you'll need a few dependencies:

$ pip install requests beautifulsoup4 pipelib

Then run:

$ python .github/scripts/update_biocontainers.py

from the root.

Expected content

Refer to the documentation for a list of the container.yaml fields, especially the required ones. A pull-request that doesn't contain the required fields will have changes requested to add them.

This registry is only for container images freely available. We can't accept container.yaml for private or access-restricted containers.

Furthermore, consider the following tips when making the pull-request:

Ideally, the container tags listed in container.yaml should be actual versions, not generic latest, stable, which tend to be moving targets. Remember that containers and Singularity HPC are there for reproducibility !
The convention here is to put containers hosted on the Docker Hub at the top of the repository, e.g. ruby, rather than in a docker.io sub-directory.
By putting your name down as author, you accept you may be contacted to review further updates of the container.yaml

😁️ Contributors 😁️

We use the all-contributors tool to generate a contributors graphic below.

_{Vanessasaurus} 💻	_{Audrey Stott} 💻	_{Alec Scott} 💻	_manbat 💻	_{Marco De La Pierre} 💻	_{Alexandre Strube} 💻	_{Xavier Delaruelle} 💻
_{SarahBeecroft} 💻	_{Matthieu Muffato} 💻	_{Georgia Stuart} 💻