mirror of
https://github.com/MillironX/singularity-builds.git
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94 lines
3.5 KiB
Markdown
94 lines
3.5 KiB
Markdown
<p align="center">
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<img src="singularity-builds-artwork.svg" alt="Logo" width="400">
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</p>
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# Singularity Builds
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[](https://cloud.sylabs.io/library/millironx/default)
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[](https://github.com/MillironX/singularity-builds/blob/master/LICENSE.md)
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Definition files for building [Nextflow]-compatible [Singularity] container
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images to use in bioinformatics pipelines. Programs get containers in this
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repository if I can't find an up-to-date container that also has Nextflow's
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dependencies installed (usually `bash` and `ps` are the culprits). All of these
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images are available on the [Sylabs Cloud Library] for easy access.
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## Get started
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1. [Install Singularity]
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2. Enter the container, e.g.
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```bash
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singularity shell library://millironx/default/julia:latest
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```
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3. Execute commands, e.g.
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```shellsession
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Singularity> julia
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_
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_ _ _(_)_ | Documentation: https://docs.julialang.org
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(_) | (_) (_) |
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_ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help.
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| | | | | | |/ _` | |
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| | |_| | | | (_| | | Version 1.6.1 (2021-04-23)
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_/ |\__'_|_|_|\__'_| | Official https://julialang.org/ release
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|__/ |
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julia>
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```
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## Where else to find container images
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### State Public Health Bioinformatics (StaPH-B) Dockerfiles
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[:globe_with_meridians: Website](https://staph-b.github.io/) -
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[:octocat: GitHub](https://github.com/StaPH-B/docker-builds) -
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[:whale: Docker hub](https://hub.docker.com/u/staphb)
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All of these images are tested for Nextflow and Singularity compatability, and
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are updated on a regular basis. I've even contributed to their repository.
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### Niema Moshiri's Dockerfiles
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[:octocat: GitHub](https://github.com/Niema-Docker) -
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[:whale: Docker hub](https://hub.docker.com/u/niemasd)
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Slim bioinformatics images based on Alpine Linux with useful (but optional)
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common combinations.
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### Biocontainers Registry
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[:globe_with_meridians: Website](https://biocontainers.pro/) -
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[:octocat: GitHub](https://github.com/BioContainers/containers) -
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[:whale: Docker hub](https://hub.docker.com/u/biocontainers)
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Most of these images are already in Singularity format, and there are _a lot_ of
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tools for the picking here.
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### McDonnell Genome Institute
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[:octocat: GitHub](https://github.com/orgs/genome/repositories?language=dockerfile) -
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[:whale: Docker hub](https://hub.docker.com/u/mgibio)
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These folks make high-quality and well-maintained images for their own and
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other tools.
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## Artwork
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Artwork was designed by [@MillironX] by remixing:
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- [DNA] by Scout (Public domain)
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- [Cardboard box] by Rushtini (Public domain)
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- [Pointing Boy in Baseball Cap] by ruthirsty (Public domain)
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- [Singularity Logo] by Sylabs (BSD 3-Clause)
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[Nextflow]: https://nextflow.io
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[Singularity]: https://sylabs.io/singularity
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[Sylabs Cloud Library]: https://cloud.sylabs.io/library/millironx/default
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[Install Singularity]: https://sylabs.io/guides/3.8/admin-guide/installation.html
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[@MillironX]: https://github.com/MillironX
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[DNA]: https://openclipart.org/detail/192915/dna
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[Cardboard box]: https://openclipart.org/detail/192915/dna
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[Pointing Boy in Baseball Cap]: https://openclipart.org/detail/281363/pointing-boy-in-baseball-cap
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[Singularity Logo]: https://github.com/sylabs/singularity/blob/master/docs/logos/singularity_v3.svg
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