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adds dorado 0.8.3 no-model #1109

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@Kincekara Kincekara commented Nov 21, 2024

Closes #1073

I tried to create a minimal dorado image. It looks like cuda base image is good enough for dorado.
WSL currently supports 12.4.0 drivers for my laptop, so I use nvidia/cuda:12.4.0-base-ubuntu22.04 as the base image.
Since dorado itself comes with many prebuild libraries, it took a lot of space. The compressed image will be around 2.4 GB.

I am leaving this PR as a draft for now in case you may want to do further tests.

[2024-11-21 20:52:25.279] [info] Running: "basecaller" "dna_r10.4.1_e8.2_260bps_sup@v3.5.2" "dna_r10.4.1_e8.2_260bps-FLO_PRO114-SQK_NBD114_96_260-4000.pod5" "--emit-moves" "--max-reads" "10"
[2024-11-21 20:52:27.120] [info] > Creating basecall pipeline
[2024-11-21 20:52:27.796] [info] Calculating optimized batch size for GPU "NVIDIA RTX 2000 Ada Generation Laptop GPU" and model dna_r10.4.1_e8.2_260bps_sup@v3.5.2. Full benchmarking will run for this device, which may take some time.
[2024-11-21 20:52:31.003] [info] cuda:0 using chunk size 10000, batch size 128
[2024-11-21 20:52:32.102] [info] cuda:0 using chunk size 5000, batch size 384
[2024-11-21 20:52:36.612] [info] > Simplex reads basecalled: 1
[2024-11-21 20:52:36.612] [info] > Basecalled @ Samples/s: 9.681710e+02
[2024-11-21 20:52:36.612] [info] > Finished

Pull Request (PR) checklist:

  • Include a description of what is in this pull request in this message.
  • The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15 )
  • Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number (i.e. spades/3.12.0/Dockerfile)
    • (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
  • Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
    • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
  • Dockerfile includes the recommended LABELS
  • Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
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@Kincekara Kincekara requested a review from kapsakcj November 21, 2024 21:15
@Kincekara Kincekara marked this pull request as ready for review November 26, 2024 17:53
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[Container Request]: dorado but without models included, maybe?
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