dependencies:
- name: java
check_running: false
min_version: 17
install_instructions: |
macOS: brew install openjdk@17
Ubuntu/Debian: sudo apt-get install openjdk-17-jdk
RHEL/CentOS: sudo yum install java-17-openjdk
Or download from: https://openjdk.org/
description: Java Runtime Environment version 17+ required for Nextflow
website: https://openjdk.org/
environments:
google_colab:
install_commands:
- apt-get update -y
- apt-get install -y openjdk-21-jdk-headless
verify_command: java -version
- name: docker
check_running: true
install_instructions: |
Install Docker Desktop from https://www.docker.com/products/docker-desktop/
Or via Homebrew: brew install --cask docker
description: Container runtime for running bioinformatics workflows
website: https://www.docker.com
environments:
google_colab:
skip: true
skip_reason: "Docker is not supported in Google Colab. Nextflow will use local executor instead."
- name: nextflow
check_running: false
install_instructions: |
Install via curl: curl -s https://get.nextflow.io | bash
Or via Homebrew: brew install nextflow
description: Workflow management system for bioinformatics pipelines
website: https://get.nextflow.io
environments:
google_colab:
install_commands:
- curl -s https://get.nextflow.io | bash
- mv nextflow /usr/local/bin/
- chmod +x /usr/local/bin/nextflow
verify_command: nextflow -version
- name: syftbox
check_running: false
install_instructions: |
Install via curl: curl -fsSL https://syftbox.net/install.sh | sh
description: Software tool for system analysis and reporting
website: https://syftbox.net
environments:
google_colab:
skip: true
skip_reason: "TODO"