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Merged
merged 2 commits into from
Oct 26, 2025
Merged

add dorado 1.1.0 #1406

merged 2 commits into from
Oct 26, 2025

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@Kincekara
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@Kincekara Kincekara commented Aug 22, 2025

  • Tests were modified since basecalling models for DNA R10.4.1 4kHz data were removed.
  • Dockerfile including models was simplified
  • Updated readme.

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/build-files/samtools/1.15 )
  • Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number in build-files (i.e. docker-builds/build-files/spades/3.12.0/Dockerfile)
    • (optional) All test files are located in same directory as the Dockerfile (i.e. build-files/shigatyper/2.0.1/test.sh)
  • Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. docker-builds/build-files/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
  • Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

@Kincekara Kincekara closed this Aug 22, 2025
@Kincekara Kincekara reopened this Aug 22, 2025
@Kincekara Kincekara requested a review from kapsakcj August 22, 2025 18:50
@Kincekara Kincekara marked this pull request as ready for review August 22, 2025 18:51
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kapsakcj commented Oct 26, 2025

Was able to successfully build the no_model dockerfile locally:

$ docker_build -t kutluhan/dorado:1.1.0-no-model build-files/dorado/1.1.0-cuda12.2.0-no_model/

[lots of output redacted for brevity]

#8 10.51 [2025-10-26 15:26:58.212] [info] > Simplex reads basecalled: 1
#8 10.51 [2025-10-26 15:26:58.213] [info] > Basecalled @ Samples/s: 2.606471e+02
#8 10.51 [2025-10-26 15:26:58.214] [info] > Finished
#8 DONE 10.7s

#9 exporting to image
#9 exporting layers
#9 exporting layers 32.4s done
#9 writing image sha256:6ea91f235a80836fa5c92a289a1ce1b163f9be44f0b4f298c508fcf56d712d17 done
#9 naming to docker.io/kutluhan/dorado:1.1.0-no-model done
#9 DONE 32.5

Same with the dockerfile that includes the models:

$ docker_build -t kutluhan/dorado:1.1.0-with-models build-files/dorado/1.1.0-cuda12.2.0/

[lots of output redacted for brevity]

#10 3.019 [2025-10-26 15:36:51.371] [info] > Creating basecall pipeline
#10 461.4 [2025-10-26 15:44:29.742] [info] > Finished in (ms): 455297
#10 461.4 [2025-10-26 15:44:29.742] [info] > Simplex reads basecalled: 1
#10 461.4 [2025-10-26 15:44:29.742] [info] > Basecalled @ Samples/s: 4.476199e+00
#10 461.4 [2025-10-26 15:44:29.759] [info] > Finished
#10 DONE 462.9s

#11 [test 3/3] RUN test -s basecalled.sam
#11 DONE 0.3s

#12 exporting to image
#12 exporting layers
#12 exporting layers 45.2s done
#12 writing image sha256:eb7d1af461e9dca17146f2201ad3a32dcc7439160c4b7727777c9438e465edb3 done
#12 naming to docker.io/kutluhan/dorado:1.1.0-with-models done
#12 DONE 45.2s

FYI I resolved the merge conflict with the /README.md

As expected, the GHActions workflow failed for the dockerfile w models due to the VM running out of storage space. The other GHActions workflow ran successfully.

Planning to:

  • merge this PR
  • deploy the no_model dockerfile through our usual route
  • and will manually build and deploy the docker image containing the model files, with similar commands to last time I did this: adding dorado version 0.9.0 #1143 (comment)

@kapsakcj kapsakcj merged commit 2600c57 into StaPH-B:master Oct 26, 2025
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kapsakcj commented Oct 26, 2025

Deploy workflow here for no_model dockerfile: https://github.com/StaPH-B/docker-builds/actions/runs/18820242340

Local building and pushing of dockerfile with model files (these commands all ran successfully):

docker_build --target app -t staphb/dorado:1.1.0-cuda12.2.0 build-files/dorado/1.1.0-cuda12.2.0/
docker_build --target app -t staphb/dorado:latest build-files/dorado/1.1.0-cuda12.2.0/
docker_build --target app -t quay.io/staphb/dorado:1.1.0-cuda12.2.0 build-files/dorado/1.1.0-cuda12.2.0/
docker_build --target app -t quay.io/staphb/dorado:latest build-files/dorado/1.1.0-cuda12.2.0/

docker push staphb/dorado:1.1.0-cuda12.2.0
docker push staphb/dorado:latest
docker push quay.io/staphb/dorado:1.1.0-cuda12.2.0
docker push quay.io/staphb/dorado:latest

docker images now available on dockerhub and quay 🎉

@Kincekara Kincekara deleted the dorado_new branch October 27, 2025 12:17
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@Kincekara @kapsakcj