Merge pull request #30 from Sydney-Informatics-Hub/gitpod

Set up gitpod for self-directed training

.github/.gitpod.Dockerfile

@@ -0,0 +1,41 @@
+# Use the Gitpod workspace base image
+FROM gitpod/workspace-base
+
+USER root
+
+# Set environment variables
+ENV TZ=Australia/Sydney
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Set the timezone and install required utilities
+RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone && \
+    apt-get update --quiet && \
+    apt-get install --quiet --yes \
+        apt-transport-https \
+        apt-utils \
+        sudo \
+        git \
+        less \
+        wget \
+        curl \
+        tree \
+        graphviz \
+        zip \
+        unzip \
+        default-jre \
+        ca-certificates
+
+# Install Nextflow
+RUN curl -s https://get.nextflow.io | bash && \
+    chmod 755 ./nextflow && \
+    mv ./nextflow /usr/local/bin
+
+# Create .nextflow directory and set proper permissions
+RUN mkdir -p /home/gitpod/.nextflow && \
+chown -R gitpod:gitpod /home/gitpod/.nextflow
+
+# Change user back to gitpod
+USER gitpod
+
+# Set the entrypoint
+ENTRYPOINT ["/bin/bash"]

.gitignore

@@ -4,3 +4,4 @@
 results/
 work/
 site/
+.DS_Store

.gitpod.code-workspace

@@ -0,0 +1,15 @@
+{
+  "folders": [
+    {
+      "path": "."
+    }
+  ],
+  "settings": {
+    "editor.tabSize": 2,
+    "files.exclude": {
+      "**/.git": true,
+      "**/.DS_Store": true
+    },
+    "gitpod.workspaceFolder": "/workspace/hello-nextflow"
+  }
+}

.gitpod.yml

@@ -0,0 +1,71 @@
+# Custom workspace and checkout locations
+workspaceLocation: gitpod/gitpod-ws.code-workspace  # Refers to your .code-workspace file
+checkoutLocation: gitpod 
+
+# GitHub prebuild configuration
+github:
+  prebuilds:
+    # Enable prebuilds for the master/default branch
+    master: true
+    # Disable prebuilds for all branches
+    branches: false
+    # Enable prebuilds for pull requests from this repo
+    pullRequests: true
+    # Enable prebuilds for pull requests from forks
+    pullRequestsFromForks: true
+    # Disable "Review in Gitpod" comment on PRs
+    addComment: false
+    # Disable "Review in Gitpod" badge on PRs
+    addBadge: false
+
+# Docker image to use for the workspace
+image: .gitpod.Dockerfile
+
+# Tasks to execute during workspace initialisation and startup
+tasks:
+  - before: printf 'unset JAVA_TOOL_OPTIONS\n' >> $HOME/.bashrc && exit
+
+  # FOR TESTING: check out workspace in the `gitpod` branch
+  - name: Checkout gitpod branch
+    init: |
+      git fetch origin gitpod  # Fetch the latest changes for the gitpod branch
+      git checkout gitpod || git checkout -b gitpod origin/gitpod  # Switch to the gitpod branch
+
+  # Create directory structure 
+  - name: Create Directories
+    init: |
+      mkdir -p ~/hello-nextflow/part1
+      mkdir -p ~/hello-nextflow/part2
+
+# Download containers to be used in part 2 
+  - name: Download containers
+    init: |
+      docker pull quay.io/biocontainers/salmon:1.10.1--h7e5ed60_0
+      docker pull quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0
+      docker pull quay.io/biocontainers/multiqc:1.19--pyhdfd78af_0
+    command: docker run hello-world
+
+# Open docs in a web browser
+  - name: Start web server
+    command: gp ports await 23000 && gp preview https://sydney-informatics-hub.github.io/hello-nextflow/
+
+# Start the tutorial 
+  - name: Start tutorial
+    command: |
+      cd hello-nextflow
+      source $HOME/.bashrc
+      export PS1='\[\e[3;36m\]${PWD/*\//} ->\[\e[0m\] '
+      unset JAVA_TOOL_OPTIONS
+      clear
+
+# VSCode extensions to install in the workspace
+vscode:
+  extensions:
+    - codezombiech.gitignore           # Support for .gitignore files
+    - cssho.vscode-svgviewer           # SVG viewer
+    - esbenp.prettier-vscode           # Prettier for markdown formatting
+    #- EditorConfig.EditorConfig        # Support for .editorconfig
+    #- Gruntfuggly.todo-tree            # Display TODO/FIXME comments in a tree view
+    - nextflow.nextflow                # Nextflow syntax highlighting
+    - streetsidesoftware.code-spell-checker  # Spell checker for source code
+    - ms-vscode.live-server            # Live server for web development