dependencies:
- name: brew
check_running: false
package_manager: true
os_filter:
- macos
install_instructions: |
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
description: Package manager for macOS
website: https://brew.sh
environments:
macos:
install_commands:
- /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
verify_command: brew --version
- name: java
check_running: false
min_version: 17
install_instructions: |
macOS: brew install openjdk
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
ubuntu:
install_commands:
- apt-get update -y
- apt-get install -y default-jdk-headless
verify_command: java -version
macos:
install_commands:
- brew install openjdk
verify_command: java -version
arch:
install_commands:
- sudo pacman -Syu --noconfirm
- sudo pacman -S --noconfirm jdk-openjdk
verify_command: java -version
windows:
install_commands:
- winget install Microsoft.OpenJDK
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."
ubuntu:
install_commands:
- apt-get update -y
- apt-get install -y --reinstall docker.io
- systemctl enable docker || true
- systemctl start docker || true
verify_command: docker --version
macos:
install_commands:
- brew install --cask docker
verify_command: docker --version
arch:
install_commands:
- sudo pacman -Syu --noconfirm
- sudo pacman -S --noconfirm docker
verify_command: docker --version
windows:
skip: true
skip_reason: "Docker Desktop for Windows requires manual installation from docker.com"
- 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
ubuntu:
install_commands:
- curl -s https://get.nextflow.io | bash
- sudo mv nextflow /usr/local/bin/
- sudo chmod +x /usr/local/bin/nextflow
verify_command: nextflow -version
macos:
install_commands:
- brew install nextflow
verify_command: nextflow -version
arch:
install_commands:
- curl -s https://get.nextflow.io | bash
- sudo mv nextflow /usr/local/bin/
- sudo chmod +x /usr/local/bin/nextflow
verify_command: nextflow -version
windows:
skip: true
skip_reason: "Nextflow doesn't have a Windows CLI installer. Please use WSL or Docker to run Nextflow on Windows"
- name: syftbox
check_running: false
install_instructions: |
Install via curl: curl -fsSL https://syftbox.net/install.sh | sh
description: An open-source network for privacy-first, offline-capable data science collaboration
website: https://syftbox.net
environments:
google_colab:
install_commands:
- curl -fsSL https://syftbox.net/install.sh | sh -s -- --download-only
- mv /root/.local/bin/syftbox /usr/local/bin/ 2>/dev/null || mv ~/.local/bin/syftbox /usr/local/bin/
- chmod +x /usr/local/bin/syftbox
verify_command: syftbox -v
ubuntu:
install_commands:
- curl -fsSL https://syftbox.net/install.sh | sh -s -- --download-only
verify_command: syftbox -v
macos:
install_commands:
- curl -fsSL https://syftbox.net/install.sh | sh -s -- --download-only
verify_command: syftbox -v
arch:
install_commands:
- curl -fsSL https://syftbox.net/install.sh | sh -s -- --download-only
verify_command: syftbox -v
windows:
skip: true
skip_reason: "SyftBox for Windows requires manual installation from GitHub releases"
- name: uv
check_running: false
install_instructions: |
Install via curl: curl -LsSf https://astral.sh/uv/install.sh | sh
Or via PowerShell: powershell -c "irm https://astral.sh/uv/install.ps1 | iex"
description: Fast Python package installer and virtualenv manager
website: https://astral.sh/uv
environments:
google_colab:
install_commands:
- which uv || (curl -LsSf https://astral.sh/uv/install.sh | sh && mv $HOME/.cargo/bin/uv /usr/local/bin/uv 2>/dev/null || mv $HOME/.local/bin/uv /usr/local/bin/uv 2>/dev/null || true)
- chmod +x /usr/local/bin/uv 2>/dev/null || true
verify_command: uv --version
ubuntu:
install_commands:
- curl -LsSf https://astral.sh/uv/install.sh | sh
- export PATH="$HOME/.cargo/bin:$PATH"
verify_command: uv --version
macos:
install_commands:
- curl -LsSf https://astral.sh/uv/install.sh | sh
- export PATH="$HOME/.cargo/bin:$PATH"
verify_command: uv --version
arch:
install_commands:
- curl -LsSf https://astral.sh/uv/install.sh | sh
- export PATH="$HOME/.cargo/bin:$PATH"
verify_command: uv --version
windows:
install_commands:
- winget install --id=astral-sh.uv -e --silent --accept-package-agreements --accept-source-agreements
verify_command: if (Get-Command uv -ErrorAction SilentlyContinue) { exit 0 } elseif (Test-Path "$env:LOCALAPPDATA\Programs\uv\uv.exe") { exit 0 } elseif (Test-Path "$env:LOCALAPPDATA\uv\bin\uv.exe") { exit 0 } elseif (Test-Path "$env:USERPROFILE\.cargo\bin\uv.exe") { exit 0 } else { exit 1 }