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Thomas A. Christensen II 593b7f222c
Add combined Julia and bam-readcounts Dockerfile 
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
2021-11-15 12:21:34 -06:00
.vscode Speed up vscode 2021-09-07 09:46:42 -05:00
assembly_improvement Give assembly_improvement a pretty README 2021-08-10 17:50:08 -05:00
clique-snv Add CliqueSNV 2021-08-31 14:12:33 -05:00
htslib Add libcurl to permenent dependencies for HTSlib 2021-09-07 11:44:02 -05:00
julia Add dockerfile for Julia image 2021-09-09 15:12:30 -05:00
julia_bam-readcounts Add combined Julia and bam-readcounts Dockerfile 2021-11-15 12:21:34 -06:00
minimap_plus Add minimap2 2021-08-17 11:59:29 -05:00
pigz Correct pigz version number 2021-08-10 18:07:42 -05:00
ray Give Ray a pretty README 2021-08-10 18:11:20 -05:00
samtools Add Samtools 2021-08-17 11:21:23 -05:00
shorah Add ShoRAH image 2021-09-07 12:27:57 -05:00
varscan Give VarScan a pretty README 2021-08-10 18:16:35 -05:00
velvet Fix Velvet container link 2021-08-10 18:21:12 -05:00
.gitattributes Fix gitattributes 2021-08-10 13:24:05 -05:00
.gitignore Basic Ray Image 2021-06-14 16:16:15 -05:00
LICENSE.md Create LICENSE.md 2021-08-10 16:51:34 -05:00
README.md Add other container sources to README 2021-09-09 15:44:31 -05:00
singularity-builds-artwork.svg Make pretty README 2021-08-10 17:34:08 -05:00

README.md

Logo

Singularity Builds

Sylabs Cloud Library MIT License

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.

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

  3. 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

:octocat: GitHub - 🐳 Docker hub

These folks make high-quality and well-maintained images for their own and other tools.

Artwork

Artwork was designed by @MillironX by remixing: