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@pinin4fjords pinin4fjords commented Mar 20, 2025

Re-pitching #539 in light of recent changes. I'll pull updates to docs etc from there once people are happy with the approach.

Local devcontainers usage means making the host file paths valid within the container to appease docker-outside-docker. This is really just a case of:

  1. Mount the host systems
  2. Use symlinking to make /workspaces/training valid and consistent with materials, and add some options to move new terminal starting dirs to the symlink.

I'm not sure if this will all work without a local build, so

I also had to pin the java version ('latest' didn't work for me).

<     "workspaceFolder": "/workspaces/training",
---
>     "workspaceFolder": "${localWorkspaceFolder}",
>     "workspaceMount": "source=${localWorkspaceFolder},target=${localWorkspaceFolder},type=bind",
27c28
<         "NXF_HOME": "/workspaces/.nextflow",
---
>         "NXF_HOME": "/workspaces/training/.nextflow",
34c35,36
<     "onCreateCommand": "bash .devcontainer/setup.sh",
---
>     "onCreateCommand": "bash ${localWorkspaceFolder}/.devcontainer/setup.sh",
>     "postCreateCommand": "mkdir -p /workspaces && rm -rf /workspaces/training && ln -s ${localWorkspaceFolder} /workspaces/training",
40c42,44
<                 "python.defaultInterpreterPath": "/opt/conda/bin/python"
---
>                 "python.defaultInterpreterPath": "/opt/conda/bin/python",
>                 "terminal.integrated.cwd": "/workspaces/training",
>                 "terminal.integrated.defaultLocation": "workspace"

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@pinin4fjords pinin4fjords requested a review from ewels March 20, 2025 13:13
@vdauwera
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@pinin4fjords where do we stand on this?

@vdauwera vdauwera added question Further information is requested environment Devcontainer, codespaces etc labels Apr 14, 2025
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@vdauwera ready to roll from my point of view. @ewels wanted to review when he could.

@vdauwera vdauwera removed the question Further information is requested label Apr 15, 2025
maxulysse
maxulysse previously approved these changes Apr 25, 2025
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Minor comment, but I followed the guide, and managed to run a different nextflow version in my local devcontainers compared to my own local install.
This is some serious magic

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Applying maxime's little suggestions dismissed his approval, but this is tested and ready to go.

@pinin4fjords pinin4fjords merged commit 073757c into master Apr 25, 2025
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@pinin4fjords pinin4fjords deleted the local-devcontainers branch April 25, 2025 16:27
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5 participants