Missing pyabpoa in Docker image

[zhengxinchang]

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Describe the bug A clear and concise description of what the bug is including the command that you have run.

Logging Please attach any relevant logging messages. (Use ``` before and after code blocks).

Environment (if you do not have a GPU, write No GPU):

• Installation method [from github source, pypi (pip install), conda]
• OS: CentOS7
• medaka version 1.11.3
• GPU model
• Nvidia driver version
• CUDA version
• cuDNN version

Additional context Add any other context about the problem here.

I am writing to report a potential bug when running medaka tandem by using Docker image.

I built the singularity image based on the Docker image and run the image as follows:

singularity exec -f -B /run:/run  --bind /stornext/:/stornext/ /softwares/medaka/medaka.sif    medaka tandem  --model res_medaka_tandem_r1041_e82_400bps_sup_v420.tar.gz  input.bam hg38_allchr_fixchrMT.fa ./adotto_TRregions_v1.2.bed.small   male test_out

Error returned from madaka

Traceback (most recent call last):
  File "/home/epi2melabs/conda/bin/medaka", line 8, in <module>
    sys.exit(main())
  File "/home/epi2melabs/conda/lib/python3.8/site-packages/medaka/medaka.py", line 814, in main
    args.func(args)
  File "/home/epi2melabs/conda/lib/python3.8/site-packages/medaka/tandem.py", line 804, in main
    raise RuntimeError(
RuntimeError: pyabpoa >= 1.4.1 is not installed. Refer to abpoa documentation at https://github.com/yangao07/abPOA for installation instructions.

I try to install the pyabpoa in the docker container and rebuild it. It seems works well.

Thanks Xinchang

[cjw85]

Hi @zhengxinchang,

Thank you for reporting this. The medaka tandem command is a little experimental, and relies on abpoa whereas the rest of medaka does not. This is why the import is optional. Unfortunately we cannot add pyapoa as a requirement to medaka in the natural way because the pyapoa package is itself broken (https://github.com/yangao07/abPOA/issues/41).

[zhengxinchang]

Hi @cjw85,

Thank you for your response! I have a question: is it possible to run Medaka tandem without using pyapoa? I've encountered an issue related to a concurrency error. While I'm not entirely certain that this problem is connected to pyapoa, I'm interested in trying Medaka without it to see if there's any change.

[cjw85]

It is not possible to run medaka tandem without pyabpoa: its inclusion as a requirement in medaka is solely for its use in medaka tandem.