Dockerfile fails: process "/bin/sh -c mamba env update -n base -f hostile/environment.yml" did not complete successfully

bede / hostile

Precise host read removal

MIT License

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Dockerfile fails: process "/bin/sh -c mamba env update -n base -f hostile/environment.yml" did not complete successfully #43

Closed dterumalai closed 2 months ago

dterumalai commented 2 months ago

Dear maintainer,

Since today, when I am trying to build the docker image using your Dockerfile, I am experiencing issues:

Dockerfile:4
--------------------
   2 |     FROM condaforge/miniforge3:latest
   3 |     RUN git clone https://github.com/bede/hostile.git
   4 | >>> RUN mamba env update -n base -f hostile/environment.yml
   5 |     RUN pip install ./hostile[dev]
   6 |     RUN cd hostile && pytest
--------------------
ERROR: failed to solve: process "/bin/sh -c mamba env update -n base -f hostile/environment.yml" did not complete successfully: exit code: 1

Any idea on what is going wrong?

Best, Dillenn

bede commented 2 months ago

Thanks for flagging this @dterumalai, I've reproduced. It's a classic case of conda deps becoming unsolvable over time. Hopefully I can fix by bumping versions, but failing that I will make a Dockerfile without reliance on conda.

In case you are in a hurry, the key non-python deps are:

samtools>=1.17
minimap2>=2.26
bowtie2>=2.4.5
bedtools (needed only for masking)

Pre built containers: https://biocontainers.pro/tools/hostile

dterumalai commented 2 months ago

Hi @bede, Thanks for the quick answer. Happy that you managed to reproduce the issue and identified the problem. I am not in a rush so I will wait for your fix.

Have a nice day!

bede commented 2 months ago

Thanks for your patience, I believe that the issue was caused by the latest Miniforge using Python 3.12. I've now pinned a compatible base image – feel free to reopen if you still have problems.