Skip to content

Latest commit

 

History

History
104 lines (78 loc) · 4.17 KB

DEVCONTAINER.md

File metadata and controls

104 lines (78 loc) · 4.17 KB

Using nf-neuro development containers

nf-neuro comes preloaded with a set of development containers destined at streamlining your development. They provide pre-installed environments for you to start programming new pipelines or nf-neuro components.

Requirements

Configuring Docker for easy usage

The simplest way of installing everything Docker is to use Docker Desktop. You can also go the engine way and install Docker manually.

Once installed, you need to configure some access rights to the Docker daemon. The easiest way to do this is to add your user to the docker group. This can be done with the following command :

sudo groupadd docker
sudo usermod -aG docker $USER

After running this command, you need to log out and log back in to apply the changes.

Prototyping environment

Warning

The prototyping environment definition is not meant to be run from the nf-neuro repository root. Locate your project elsewhere (we recommend putting it outside this directory to prevent conflicts with git).

Usage

Copy the devcontainer definition located in .devcontainer/prototyping inside a .devcontainer directory inside your project. Then, open your project with VS CODE and click on the blue box in the lower left corner, to get a prompt to Reopen in container. The procedure will start a docker build, wait for a few minutes and enjoy your fully configured development environment.

Available in the container

  • nf-core accessible through the terminal, which is configured to access nf-neuro modules and subworkflows
  • git, github-cli
  • curl, wget, apt-get
  • nextflow, docker, tmux

Available in the VS Code IDE through extensions

  • Docker images and containers management
  • Nextflow execution environemnt
  • Python and C++ linting, building and debugging tools
  • Github Pull Requests management
  • Github flavored markdown previewing
  • Neuroimaging data viewer
  • Test Data introspection
  • Resource monitoring
  • Remote development
  • Live sharing with collaborators

Production environment

SECTION TO COME

Development environment

Usage

To use the development environment, you need to have the repository cloned. You can do it using VS Code. Once opened in VS CODE, click on the arrow box in the lower left corner, to get a prompt to Reopen in container. Select the devops container. The procedure will start a docker build, wait for a few minutes and enjoy your fully configured development environment.

Available in the container

  • nf-neuro, nf-core all accessible through the terminal, which is configured to load the poetry environment in shells automatically
  • nf-neuro configured as the main repository for all nf-core commands, using NFCORE_- environment variables
  • git, github-cli
  • curl, wget, apt-get
  • nextflow, nf-test, docker, tmux

Available in the VS Code IDE through extensions

  • Docker images and containers management
  • Nextflow execution environemnt
  • Python and C++ linting, building and debugging tools
  • Github Pull Requests management
  • Github flavored markdown previewing
  • Neuroimaging data viewer
  • Test Data introspection
  • Resource monitoring
  • Remote development
  • Live sharing with collaborators