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Docker Build Not Working #6

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SFD5311 opened this issue Aug 30, 2023 · 0 comments
Open

Docker Build Not Working #6

SFD5311 opened this issue Aug 30, 2023 · 0 comments

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@SFD5311
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SFD5311 commented Aug 30, 2023

Attempting to test fixes for some recent failures for the celldive pipeline, I was not able to build the docker image for celldive-scripts on my machine or on the HIVE cluster. The build fails on the step with:
RUN conda env update -f /tmp/environment.yml

It appears to be an issue with dependencies, although the conda output isn't terribly informative. A docker build using pip and a requirements.txt file based on a pip freeze from the release docker image was also unsuccessful. I did have some success with docker builds using a minimal set of python packages (ones imported in the relevant scripts), using pip show to get the versions from the release docker image.

I think this could also be a good opportunity to align the docker builds more closely with those used in the salmon-rnaseq and sc-atac-seq-pipelines (using pip for managing dependencies and subdirectories for each docker image containing a Dockerfile and requirements.txt if applicable)

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