Referencing Biocontainers Links in Manual

[jamesbraza]

The manual section Obtaining Bowtie 2 suggests using Biocontainers via Docker Hub.

Biocontainers has a lot of containers available (see BioContainers/containers). It would be nice to suggest some possible containers to try, to help get people started.

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BioContainers I Found

Looks like BioContainers support bowtie2 here (GitHub) --> here (Docker Hub). The last bowtie2 image was made in 2020 for bowtie2 version 2.4.1.

[smdabdoub]

https://quay.io/repository/biocontainers/bowtie2?tab=tags

[pmambrose]

I made a dockerfile for v2.5.2 native for Apple M1/2/3 silicon (arm64) if anyone finds it useful, as that's my primary laptop and an arch64 version of bowtie2 is available, so I figured why not. It works great on my M1. There's also a dockerfile for an equivalent amd64 build but I haven't tested that one:

https://github.com/pmambrose/docker-bowtie2

Those quay.io and dockerhub containers are amd64 only I think, as are all the packages on Bioconda so I couldn't generate a native one by adding bowtie2 to an existing arm64 conda docker image. If it would be helpful to publish it to dockerhub or quay or add it to this repository somehow let me know! I'm pretty new with docker, I'll have to learn how to do any of that.

[jamesbraza]

@pmambrose @smdabdoub if you have time to review a PR, I have made https://github.com/BenLangmead/bowtie2/pull/462 which upstreams this info, thank you both for sharing info

[smdabdoub]

@jamesbraza Looks great! The only thing you might consider adding is that Singularity/Apptainer containers can be created from the Docker containers using the singularity pull command, for example:

singularity pull docker://quay.io/biocontainers/bowtie2:2.5.2--py39h6fed5c7_0

[jamesbraza]

I haven't heard of Singularity or Apptainer before, TIL :). Am I correct that they're "downstream" infrastructure from Bowtie 2? I think the Bowtie 2 docs should not about infrastructure possibilities beyond the base Docker image.

Edit: I decided to add a docker pull just to show how one can pull, but staying closer to Docker itself.

[smdabdoub]

Singularity is essentially just Docker optimized for cluster computing.

[pmambrose]

@jamesbraza looks great to me! Thank you for putting this together! Let me know if there's anything additional I can help with. If it will be useful I can try publishing the container on dockerhub or quay.