Fixed the Dockerfile - Githubissues

HadrienG / InSilicoSeq

:rocket: A sequencing simulator

https://insilicoseq.readthedocs.io

MIT License

176 stars 32 forks source link

Fixed the Dockerfile #251

Closed StefanLelieveld closed 4 months ago

StefanLelieveld commented 4 months ago

Issue: Docker-image is not working correctly for v2.0.0 (locally). And is not working on https://hub.docker.com/r/hadrieng/insilicoseq

Updated the Dockerfile: The v2.0.0 docker image works.
Added script docker-build.sh: Builds a multi architecture Docker-image for AMD and ARM. @HadrienG I have left the REGISTRY value open in the script for you to fill in. I have tested the script on our docker-registry and as far as I could test it worked. Please let me know if it does the trick for you too.

HadrienG commented 4 months ago

Thanks @StefanLelieveld . If we go this route I'd also like to automate this with github actions.

Alternatively, I'm wondering why would we still maintain this instead of pointing to the biocontainer that bioconda builds automatically? then all we have to do is change all the paths to quay.io/biocontainers/insilicoseq:2.0.0--pyh7cba7a3_0 in the documentation.

Lemme know what you think /Hadrien

StefanLelieveld commented 4 months ago

Thanks @StefanLelieveld . If we go this route I'd also like to automate this with github actions.

Alternatively, I'm wondering why would we still maintain this instead of pointing to the biocontainer that bioconda builds automatically? then all we have to do is change all the paths to quay.io/biocontainers/insilicoseq:2.0.0--pyh7cba7a3_0 in the documentation.

Lemme know what you think /Hadrien

Hi Hadrien,

I just had a chat with Thijs and we like the alternative approach you propose. I will remove the Dockerfile + docker-build.sh and change the docker-image in the README to the biocontainer docker-image you provided.

best, Stefan

StefanLelieveld commented 4 months ago

I will remove the Dockerfile + docker-build.sh and change the docker-image in the README to the biocontainer docker-image you provided.

Update on the matter: The Biocontainer docker image is not build for the ARM architecture (only for AMD?). This might be a reason to use the Dockerfile (and multi-arch build script) to provide support for both architectures in one solution.

@HadrienG @ThijsMaas what would your opinion? Support ARM architectures too?

HadrienG commented 4 months ago

We're a pure python package. The biocontainer works on my ARM mac despite being built for amd64