mirror of
https://github.com/MillironX/singularity-builds.git
synced 2024-12-21 12:28:17 +00:00
94 lines
3.5 KiB
Markdown
94 lines
3.5 KiB
Markdown
<p align="center">
|
|
<img src="singularity-builds-artwork.svg" alt="Logo" width="400">
|
|
</p>
|
|
|
|
# Singularity Builds
|
|
|
|
[](https://cloud.sylabs.io/library/millironx/default)
|
|
[](https://github.com/MillironX/singularity-builds/blob/master/LICENSE.md)
|
|
|
|
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
|
|
|
|
1. [Install Singularity]
|
|
2. Enter the container, e.g.
|
|
|
|
```bash
|
|
singularity shell library://millironx/default/julia:latest
|
|
```
|
|
|
|
3. Execute commands, e.g.
|
|
|
|
```shellsession
|
|
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
|
|
|
|
[:globe_with_meridians: Website](https://staph-b.github.io/) -
|
|
[:octocat: GitHub](https://github.com/StaPH-B/docker-builds) -
|
|
[:whale: Docker hub](https://hub.docker.com/u/staphb)
|
|
|
|
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](https://github.com/Niema-Docker) -
|
|
[:whale: Docker hub](https://hub.docker.com/u/niemasd)
|
|
|
|
Slim bioinformatics images based on Alpine Linux with useful (but optional)
|
|
common combinations.
|
|
|
|
### Biocontainers Registry
|
|
|
|
[:globe_with_meridians: Website](https://biocontainers.pro/) -
|
|
[:octocat: GitHub](https://github.com/BioContainers/containers) -
|
|
[:whale: Docker hub](https://hub.docker.com/u/biocontainers)
|
|
|
|
Most of these images are already in Singularity format, and there are _a lot_ of
|
|
tools for the picking here.
|
|
|
|
### McDonnell Genome Institute
|
|
|
|
[:octocat: GitHub](https://github.com/orgs/genome/repositories?language=dockerfile) -
|
|
[:whale: Docker hub](https://hub.docker.com/u/mgibio)
|
|
|
|
These folks make high-quality and well-maintained images for their own and
|
|
other tools.
|
|
|
|
## Artwork
|
|
|
|
Artwork was designed by [@MillironX] by remixing:
|
|
|
|
- [DNA] by Scout (Public domain)
|
|
- [Cardboard box] by Rushtini (Public domain)
|
|
- [Pointing Boy in Baseball Cap] by ruthirsty (Public domain)
|
|
- [Singularity Logo] by Sylabs (BSD 3-Clause)
|
|
|
|
[Nextflow]: https://nextflow.io
|
|
[Singularity]: https://sylabs.io/singularity
|
|
[Sylabs Cloud Library]: https://cloud.sylabs.io/library/millironx/default
|
|
[Install Singularity]: https://sylabs.io/guides/3.8/admin-guide/installation.html
|
|
[@MillironX]: https://github.com/MillironX
|
|
[DNA]: https://openclipart.org/detail/192915/dna
|
|
[Cardboard box]: https://openclipart.org/detail/192915/dna
|
|
[Pointing Boy in Baseball Cap]: https://openclipart.org/detail/281363/pointing-boy-in-baseball-cap
|
|
[Singularity Logo]: https://github.com/sylabs/singularity/blob/master/docs/logos/singularity_v3.svg
|