Neurodocker
Neurodocker defines the instructions to install and configure software using YAML files. These files are known as templates. This page explains how to add a new template to Neurodocker.
The env and instructions values can use Jinja2 template language.
env
instructions
This example installs jq, a command-line JSON processor.
jq
# The name of the software. This becomes the name in the template registry. # The CLI option would be rendered as `--jq`. name: jq # An alert that is printed when using this template in the CLI. alert: Please be advised that this software uses # How to install this software from pre-compiled binaries. binaries: # The available versions and their corresponding urls. urls: "1.6": https://github.com/stedolan/jq/releases/download/jq-1.6/jq-linux64 "1.5": https://github.com/stedolan/jq/releases/download/jq-1.5/jq-linux64 # Arguments that the user can provide when using this template. These arguments # should be referenced in the `env` and/or `instructions`. arguments: required: - version optional: install_path: /opt/jq-{{ self.version }} # Environment variables to set in the container. Keys and values must be strings. env: PATH: {{ self.install_path }}:$PATH # System packages that this software depends on. dependencies: apt: - ca-certificates - curl yum: - curl # The installation instructions. Think of this like a shell scripts that installs # the software. instructions: | {{ self.install_dependencies() }} mkdir -p {{ self.install_path }} curl -fsSL --output {{ self.install_path }}/jq {{ self.urls[self.version]}} chmod +x {{ self.install_path }}/jq