-
Notifications
You must be signed in to change notification settings - Fork 213
Local devcontainers enablement #539
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Closed
+187
−44
Closed
Changes from 9 commits
Commits
Show all changes
22 commits
Select commit
Hold shift + click to select a range
aa6dbdd
Local devcontainers enablement
pinin4fjords db07194
Don't symlink
pinin4fjords dcc3367
Fix postcreate
pinin4fjords d4fe3e3
Add missing comma
pinin4fjords 21d5d6f
Remove unnecessary line
pinin4fjords 7ce3608
Remove unnecessary line
pinin4fjords 267622a
Remove unnecessary line
pinin4fjords 595168b
Remove superfluous comments
ewels a29a5e4
Remove defunct svg viewer extension
ewels 56e300c
Cross-arch fixes for local devcontainer (e.g. Mac)
pinin4fjords 1f79ad7
Docs updates
pinin4fjords 5a07633
Prettier
pinin4fjords 7ff6464
Prettier
pinin4fjords 3488dc4
Add to mkdocs
pinin4fjords cb6169f
Prettier
pinin4fjords 957ab43
Fix img link
pinin4fjords 460de86
Formatting fixes
pinin4fjords f3e3bd4
Prettier
pinin4fjords 8d69d56
Change title
pinin4fjords 30fcf73
Merge branch 'master' into local_devcontainer
pinin4fjords e33405d
Remove VSCode extensions that are part of the nf-core extension pack
ewels 80f656a
Fix pre commit
ewels File filter
Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
There are no files selected for viewing
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,34 @@ | ||
{ | ||
"name": "nextflow-training (codespaces)", | ||
|
||
// Update this to pin the release tag before release | ||
"image": "ghcr.io/nextflow-io/training:latest", | ||
// Uncomment this and comment "image" when testing Dockerfile changes | ||
// "build": { "dockerfile": "../Dockerfile", "context": ".." }, | ||
|
||
"features": { | ||
"ghcr.io/devcontainers/features/docker-outside-of-docker:1": { | ||
"version": "latest" | ||
} | ||
}, | ||
"workspaceFolder": "/workspaces/training", | ||
"remoteEnv": { | ||
"NXF_HOME": "/workspaces/.nextflow", | ||
"HOST_PROJECT_PATH": "/workspaces/training" | ||
}, | ||
"customizations": { | ||
"vscode": { | ||
"settings": { | ||
"python.defaultInterpreterPath": "/opt/conda/bin/python" | ||
}, | ||
"extensions": [ | ||
"ms-python.python", | ||
"ms-python.vscode-pylance", | ||
"nf-core.nf-core-extensionpack", // nf-core recommended extensions | ||
"nextflow.nextflow", // Nextflow VS Code extension | ||
"codezombiech.gitignore" // Language support for .gitignore files | ||
ewels marked this conversation as resolved.
Show resolved
Hide resolved
|
||
] | ||
} | ||
}, | ||
"remoteUser": "root" | ||
} |
ewels marked this conversation as resolved.
Show resolved
Hide resolved
|
This file was deleted.
Oops, something went wrong.
ewels marked this conversation as resolved.
Show resolved
Hide resolved
|
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1 @@ | ||
./codespaces/devcontainer.json |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,38 @@ | ||
{ | ||
"name": "nextflow-training (local)", | ||
|
||
// Update this to pin the release tag before release | ||
"image": "ghcr.io/nextflow-io/training:latest", | ||
// Uncomment this and comment "image" when testing Dockerfile changes | ||
// "build": { "dockerfile": "../Dockerfile", "context": ".." }, | ||
|
||
"features": { | ||
"ghcr.io/devcontainers/features/docker-outside-of-docker:1": { | ||
"version": "latest" | ||
} | ||
}, | ||
"workspaceFolder": "${localWorkspaceFolder}", | ||
"workspaceMount": "source=${localWorkspaceFolder},target=${localWorkspaceFolder},type=bind", | ||
"remoteEnv": { | ||
"NXF_HOME": "/workspaces/training/.nextflow", | ||
"HOST_PROJECT_PATH": "/workspaces/training" | ||
}, | ||
"postCreateCommand": "sudo mkdir -p /workspaces && sudo rm -rf /workspaces/training && sudo ln -s ${localWorkspaceFolder} /workspaces/training", | ||
"customizations": { | ||
"vscode": { | ||
"settings": { | ||
"python.defaultInterpreterPath": "/opt/conda/bin/python", | ||
"terminal.integrated.cwd": "/workspaces/training", | ||
"terminal.integrated.defaultLocation": "workspace" | ||
}, | ||
"extensions": [ | ||
"ms-python.python", | ||
"ms-python.vscode-pylance", | ||
"nf-core.nf-core-extensionpack", // nf-core recommended extensions | ||
"nextflow.nextflow", // Nextflow VS Code extension | ||
"codezombiech.gitignore" // Language support for .gitignore files | ||
ewels marked this conversation as resolved.
Show resolved
Hide resolved
|
||
] | ||
} | ||
}, | ||
"remoteUser": "root" | ||
} |
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Uh oh!
There was an error while loading. Please reload this page.