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atarashansky / SAMap

SAMap: Mapping single-cell RNA sequencing datasets from evolutionarily distant organisms.
MIT License
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SAMap and Docker #115

Closed avianalter closed 1 year ago

avianalter commented 1 year ago

A SAMap Docker image doesn't really exist (EDIT: never mind - there is one on Dockerhub, https://hub.docker.com/r/tarashan/samap, just no Dockerfile available). The basic jupyter and samapGUI functions work in that image, but the image doesn't have the ability to generate h5ad files using that image's environment (cf #78), so I pulled the above image and added R + some packages including Seurat, sceasy, and reticulate, which I was using to convert Seurat-processed 10X data into AnnData files.

https://hub.docker.com/r/avianalter/samap

atarashansky commented 1 year ago

Hi @avianalter ! That docker image is quite old - I removed the Dockerfile since I didn't have the bandwidth to maintain it. Did you update the version of SAMap to the latest in the docker image?

avianalter commented 1 year ago

@atarashansky very understandable re: the Dockerfile.

Originally, I installed everything from scratch into a new Docker image with a Dockerfile I wrote. Got everything to work, but the SAMGUI functionality was broken. Wasted entirely too much time in dependency hell trying to get plotly to play nice with Jupyter so I decided to just try your Docker image instead and got everything to work.

That being said, I just upgraded the SAMap version in the image manually and then pushed it to Dockerhub just now. I'm a bit too scared to use setuptools because I'm worried it will break a bunch of dependencies, so I literally just copy/pasted the newest *.py files into the miniconda installation. Ran your vignette in Jupyter and the import, SAM initialization, SAMAP, and SAMGUI functionalities worked fine.

Thanks for the software!