Florian Wuennemann
06/25/2025, 1:23 PM-profile docker or trying to execute an nf-test with --profile=+docker results in the following in codespaces for me:
Command error:
docker: Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?.
See 'docker run --help'.
This can be easily fixed by including the following snippets in the devcontainer.json file:
"features": {
"<http://ghcr.io/devcontainers/features/docker-outside-of-docker:1|ghcr.io/devcontainers/features/docker-outside-of-docker:1>": {
"version": "latest"
}
},
If we truly don't have this included at the moment, I suggest adding it with a future template update, as docker usage in codespaces is an important part of developing and testing pipelines!Florian Wuennemann
06/25/2025, 1:49 PM{
"name": "nfcore",
"image": "nfcore/gitpod:latest",
"remoteUser": "gitpod",
"runArgs": ["--privileged"],
"features": {
"<http://ghcr.io/devcontainers/features/docker-outside-of-docker:1|ghcr.io/devcontainers/features/docker-outside-of-docker:1>": {
"version": "latest"
}
},
// Configure tool-specific properties.
"customizations": {
// Configure properties specific to VS Code.
"vscode": {
// Set *default* container specific settings.json values on container create.
"settings": {
"python.defaultInterpreterPath": "/opt/conda/bin/python"
},
// Add the IDs of extensions you want installed when the container is created.
"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
}
}
}mashehu
06/25/2025, 1:56 PMFlorian Wuennemann
06/25/2025, 2:02 PM