Local installation using VSCode Devcontainers extension¶

If you have a local Docker installation or are happy to install one, the easiest way to work locally with these materials is to use Visual Studio Code's devcontainer feature. This approach provides all the necessary tools and dependencies without requiring manual installation.

Requirements¶

To use the devcontainer setup, you'll need:

Visual Studio Code
A local Docker installation, for example:
Docker Desktop (for Windows/macOS)
Docker Engine (for Linux)
Colima (alternative for macOS)
Docker Buildx (included in Docker Desktop, but may need separate installation with other Docker setups)
Dev Containers extension for VS Code

Your Docker installation must be running before you attempt to open the devcontainer.

To verify that Docker buildx is available, run:

docker buildx version

If this command fails, you'll need to install the buildx extension before proceeding.

Setup Instructions¶

Follow these steps to set up your local environment using VS Code devcontainers:

Install the "Dev Containers" extension in VS Code¶

Open VS Code
Go to Extensions (Ctrl+Shift+X or Cmd+Shift+X on macOS)
Search for "Dev Containers"
Click "Install"

Installing Dev Containers extension in VS Code

Clone the repository:¶

git clone https://github.com/nextflow-io/training.git
cd training

Open the repository in VS Code:¶

Launch VS Code
Select File -> Open Folder from the menu
Navigate to and select the training repository folder you just cloned
Click Open

Reopen in Container¶

If prompted by VS Code to "Reopen in Container", click on it. Alternatively:

Press F1 (or Ctrl+Shift+P / Cmd+Shift+P on macOS)
Type "Dev Containers: Reopen in Container"
Important: When prompted to select a configuration, choose the local-dev devcontainer configuration

Reopen in Container prompt

Selecting local configuration

Wait for the container to build. This may take a few minutes the first time as it downloads and sets up all the necessary components.

Once the container is built and running, you'll have a fully configured environment with all the necessary tools installed, including:

Java
Nextflow
Docker
Git
And all other dependencies required for the training

VS Code with devcontainer running

Benefits of Using Devcontainers¶

Using the devcontainer approach offers several advantages:

Consistency: Ensures a consistent development environment across different machines
Simplicity: All dependencies are pre-installed and configured
Isolation: The development environment is isolated from your local system
Reproducibility: Everyone using the devcontainer gets the same setup
No manual installation: No need to manually install Java, Nextflow, and other tools

Checking Your Environment¶

Once your devcontainer is running, you can verify that everything is set up correctly by running:

nextflow info

This should display the Nextflow version and runtime information, confirming that your environment is properly configured.

Troubleshooting¶

If you encounter issues with the devcontainer setup:

Ensure your Docker installation (Docker Desktop, Colima, Docker Engine, etc.) is running before opening the devcontainer
Check that you've selected the local-dev configuration when prompted
Verify that Docker buildx is installed and working by running docker buildx version
If the container fails to build, try rebuilding it by running the "Dev Containers: Rebuild Container" command
For persistent issues, refer to the VS Code Dev Containers troubleshooting guide