diff --git a/.gitpod.yml b/.gitpod.yml deleted file mode 100644 index da79e25ce..000000000 --- a/.gitpod.yml +++ /dev/null @@ -1,52 +0,0 @@ -workspaceLocation: gitpod/gitpod-ws.code-workspace -checkoutLocation: gitpod - -github: - prebuilds: - # enable for the master/default branch (defaults to true) - master: true - # enable for all branches in this repo (defaults to false) - branches: false - # enable for pull requests coming from this repo (defaults to true) - pullRequests: true - # enable for pull requests coming from forks (defaults to false) - pullRequestsFromForks: true - # add a "Review in Gitpod" button as a comment to pull requests (defaults to true) - addComment: true - # add a "Review in Gitpod" button to pull requests (defaults to false) - addBadge: false - -# See .github/Dockerfile -image: ghcr.io/nextflow-io/training:latest - -tasks: - - before: printf 'unset JAVA_TOOL_OPTIONS\n' >> $HOME/.bashrc && exit - - - name: Start web server - command: gp ports await 23000 && gp preview https://training.nextflow.io/hello_nextflow - - - name: Load Nextflow Tutorial - command: docker pull -q nextflow/rnaseq-nf - - - name: Start Nextflow Tutorial - env: - NXF_HOME: "/workspace/gitpod/.nextflow" - command: | - cd hello-nextflow - source $HOME/.bashrc - export PS1='\[\e[3;36m\]${PWD/*\//} ->\[\e[0m\] ' - unset JAVA_TOOL_OPTIONS - clear - -vscode: - extensions: # based on nf-core.nf-core-extensionpack - - codezombiech.gitignore # Language support for .gitignore files - - cssho.vscode-svgviewer # SVG viewer - - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - # - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - - nextflow.nextflow # Nextflow syntax highlighting - # - oderwat.indent-rainbow # Highlight indentation level - - streetsidesoftware.code-spell-checker # Spelling checker for source code - - ms-vscode.live-server diff --git a/docs/envsetup/index.md b/docs/envsetup/index.md index 95c067729..c04f6dda9 100644 --- a/docs/envsetup/index.md +++ b/docs/envsetup/index.md @@ -9,3 +9,15 @@ If you already have a GitHub Codespaces account, click on the button below, othe Let's get started! [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master) + +For more detailed instructions for GitHub Codespaces, see the [GitHub Codespaces env-setup docs](01_setup.md). +If you cannot use GitHub Codespaces and wish to use a local development environment, see the [documentation for local installation](02_local.md). + +!!! info "Deprecation of GitPod" + + Nextflow Training used to use [Gitpod](https://gitpod.io) until February 2025. + However, the makers of Gitpod have decided to retire the free functionality in favor of their new [Gitpod Flex](https://www.gitpod.io/blog/introducing-gitpod-flex) system. + For that reason, we have switched to using GitHub Codespaces, which also offer a one-click developer environment with no prior setup. + + Depending on when you signed up to GitPod and when exactly they retire the service, you may still be able to launch the training in their old cloud IDE, though we cannot guarantee reliable access going forward: + [Open in Gitpod](https://gitpod.io/#https://github.com/nextflow-io/training). diff --git a/docs/index.md b/docs/index.md index 0015c4ba0..605b0cbf7 100644 --- a/docs/index.md +++ b/docs/index.md @@ -22,20 +22,11 @@ When you're ready to get down to work, click on the 'Open in GitHub Codespaces' [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master) -!!! note - - Nextflow Training used to use [Gitpod](https://gitpod.io) until February 2025. - However, the makers of Gitpod have decided to retire the free functionality in favor of their new [Gitpod Flex](https://www.gitpod.io/blog/introducing-gitpod-flex) system. - For that reason, we have switched to using GitHub Codespaces, which also offer a one-click developer environment with no prior setup. - - Depending on when you signed up to GitPod and when exactly they retire the service, you may still be able to launch the training in their old cloud IDE, though we cannot guarantee reliable access going forward: - [Open in Gitpod](https://gitpod.io/#https://github.com/nextflow-io/training). - ## Training Environment Setup !!! exercise "Environment Setup" - !!! quote inline end "" + !!! tip inline end "" :material-lightbulb: Set up your environment for the first time. @@ -49,7 +40,7 @@ These are foundational, domain-agnostic courses intended for those who are compl !!! exercise "Hello Nextflow" - !!! quote inline end "" + !!! tip inline end "" :material-run-fast: Learn to develop pipelines in Nextflow. @@ -57,12 +48,14 @@ These are foundational, domain-agnostic courses intended for those who are compl [Launch the Hello Nextflow training :material-arrow-right:](hello_nextflow/index.md){ .md-button .md-button--primary } -**Coming soon:** "Nextflow Run" — Learn to run Nextflow pipelines (run only, no code development) +!!! info "" + + **Coming soon:** "Nextflow Run" — Learn to run Nextflow pipelines (run only, no code development)