adding dorado version 0.9.0

[erinyoung]

There's a new version of dorado!

According to the release notes there are some new features and bug fixes.

I imagine the one everyone is most excited about is the "polish" feature.

I copied the files from the prior version, updated the version arg, and added a wordir.

The full diff:

$ diff dorado/0.8.3/Dockerfile dorado/0.9.0/Dockerfile 
4c4
< ARG DORADO_VER=0.8.3
---
> ARG DORADO_VER=0.9.0
40a41,42
> 
> WORKDIR /data

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)
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• 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
• Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing
  \

[erinyoung]

I got this error from GA testing:

ERROR: failed to solve: failed to copy to tar: rpc error: code = Unknown desc = io: read/write on closed pipe
Error: buildx failed with: ERROR: failed to solve: failed to copy to tar: rpc error: code = Unknown desc = io: read/write on closed pipe

I haven't encountered this before and will need to do some searching to see how to fix this.

[Kincekara]

It may be a glitch in Git Hub.
Could you also try to use the cuda base image instead of devel. The last time I checked here, the cuda base could run dorado with GPU.

From https://hub.docker.com/r/nvidia/cuda

Overview of Images
Three flavors of images are provided:
base: Includes the CUDA runtime (cudart)
runtime: Builds on the base and includes the CUDA math libraries⁠, and NCCL⁠. A runtime image that also includes cuDNN⁠ is available.
devel: Builds on the runtime and includes headers, development tools for building CUDA images. These images are particularly useful for multi-stage builds.

[Kincekara]

I have just remembered GA doesn't have enough space to run this image. @kapsakcj tested and pushed the previous image manually as far as I remember.

[kapsakcj]

Yes, it doesn't build successfully on GHActions due to limited disk space.

I suggest testing the build locally on a machine that has more disk available.

I can test, but it will be a few days before I can get to it.

I would recommend switching the base image back to what it was prior

[erinyoung]

I changed the base back to nvidia/cuda:12.2.0-devel-ubuntu20.04 and moved the files to the build-files subdirectory.