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Singularity Builds

Definition files for building Nextflow-compatible Singularity container images to use in bioinformatics pipelines. Programs get containers in this repository if I can't find an up-to-date container that also has Nextflow's dependencies installed (usually bash and ps are the culprits). All of these images are available on the Sylabs Cloud Library for easy access.

Get started

Install Singularity

Enter the container, e.g.

singularity shell library://millironx/default/julia:latest

Execute commands, e.g.

Singularity> julia
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.6.1 (2021-04-23)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia>

Where else to find container images

State Public Health Bioinformatics (StaPH-B) Dockerfiles

🌐 Website - :octocat: GitHub - 🐳 Docker hub

All of these images are tested for Nextflow and Singularity compatability, and are updated on a regular basis. I've even contributed to their repository.

Niema Moshiri's Dockerfiles

:octocat: GitHub - 🐳 Docker hub

Slim bioinformatics images based on Alpine Linux with useful (but optional) common combinations.

Biocontainers Registry

🌐 Website - :octocat: GitHub - 🐳 Docker hub

Most of these images are already in Singularity format, and there are a lot of tools for the picking here.

McDonnell Genome Institute