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rcorces / ArchR_docker

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Running containerized ArchR on an HPC system #4

Open RegnerM2015 opened 2 years ago

RegnerM2015 commented 2 years ago

Hi @rcorces and @paupaiz

Building off our conversation from https://github.com/GreenleafLab/ArchR/issues/1218#issuecomment-1022400089, I am currently trying to set up a containerized ArchR analysis using Singularity on my institution's HPC system. Docker would be preferable, but as you may know, HPC systems typically do not support Docker. Therefore, I am also trying the Singularity route to run Docker images!

How do you envision this Singularity image running on an HPC system? Ideally, I would like to submit a bash script or snakemake command to run an ArchR analysis non-interactively. Thanks for your insights and help!

rcorces commented 2 years ago

Just to clarify, this repository is still pre-release. @paupaiz experienced issues getting this stuff to work with singularity on an HPC so we didnt really plan to recommend that. Instead, we plan to use an R package manager (renv) to create specific R environments that can be used from an HPC without containers.

drowsygoat commented 1 month ago

Hello. I was wondering if there has been any update on this issue. I'm need to containerize ArchR specifically for use with an HPC cluster, and I came across this repository. I understand that it's not straightforward to make ArchR work in a containerized form, but if anything like this already exists, I would be grateful for a heads up.

rcorces commented 1 month ago

No update. But we do have some things in the works and are hoping to have more ArchR-related news soon.

drowsygoat commented 1 month ago

Many thanks for fast reply. This is great news, as it's a fantastic package that, unfortunately, gave me hard time with newer R versions (for which our HPC cluster is optimized, so downgrading was not an option). Is there any existing singularity definition file that you would be agreeable to share before the "official" version is released?

RegnerM2015 commented 1 month ago

I was able to make a docker image that I could run via Singularity on an HPC environment. The image is publicly available on DockerHub: https://hub.docker.com/r/regnerm/scbreast_2023

To see how it was implemented using Singularity, you can view the git repo for our recent single-cell breast cancer paper here: https://github.com/RegnerM2015/scBreast_scRNA_scATAC_2024/wiki

I hope you find this helpful!