Requirements

To start contributing to OpenProblems, you need to have the following software installed:

Bash (>= 3.2)
Java Development Kit (>= 11)
Docker
Viash (>= 0.9.0)
Nextflow (>= 21.04)

The following sections provide instructions on how to install each of these tools. If you already have all of them installed, feel free to skip ahead to Create a component or Create a new task.

Step 1: install Bash

Bash is already included in most Debian- and Ubuntu-based distributions. If it is not installed, open a terminal and run:

sudo apt-get update
sudo apt-get install bash

Bash is already included in most RHEL- and Fedora-based distributions. If it is not installed, open a terminal and run:

sudo yum install bash

Bash is already included in most Arch-based distributions. If it is not installed, run:

sudo pacman -S bash

You will need to install Ubuntu using Windows Subsystem for Linux (WSL).

Open PowerShell or Windows Command Prompt in administrator mode by right-clicking and selecting “Run as administrator”, then run:

wsl --install

After rebooting, open Ubuntu from the Start menu. Bash is already included.

Content adapted from the WSL installation instructions.

Verify that you have Bash version 3.2 or higher:

bash --version

Step 2: install Java

You will need Oracle Java >= 11 or OpenJDK >= 11.

sudo apt-get update
sudo apt-get install openjdk-11-jdk

sudo yum install java-11-openjdk-devel

sudo pacman -S jdk11-openjdk

If you haven’t done so already, first install Homebrew:

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"

Then install Java 11:

brew install openjdk@11

Open Ubuntu in WSL and run:

sudo apt-get update
sudo apt-get install openjdk-11-jdk

Verify that you have Java version 11 or higher:

java -version

Step 3: install Docker

sudo apt update
sudo apt install docker.io
sudo systemctl enable docker
sudo usermod -aG docker $USER

On RHEL:

sudo yum install -y yum-utilities
sudo yum-config-manager \
    --add-repo \
    https://download.docker.com/linux/rhel/docker-ce.repo
sudo yum install docker-ce docker-ce-cli containerd.io docker-compose-plugin
sudo systemctl enable docker
sudo usermod -aG docker $USER

On Fedora:

sudo dnf -y install dnf-plugins-core
sudo dnf config-manager \
    --add-repo \
    https://download.docker.com/linux/fedora/docker-ce.repo
sudo dnf install docker-ce docker-ce-cli containerd.io docker-compose-plugin
sudo systemctl enable docker
sudo usermod -aG docker $USER

sudo pacman -S docker
sudo systemctl enable docker
sudo usermod -aG docker $USER

Open Ubuntu in WSL and run:

sudo apt update
sudo apt install docker.io
sudo systemctl enable docker
sudo usermod -aG docker $USER

Verify that Docker is working:

docker run hello-world

Step 4: install Viash

curl -fsSL dl.viash.io | bash
mkdir -p "$HOME/.local/bin"
mv viash "$HOME/.local/bin"

curl -fsSL dl.viash.io | bash
mkdir -p "$HOME/.local/bin"
mv viash "$HOME/.local/bin"

curl -fsSL dl.viash.io | bash
mkdir -p "$HOME/.local/bin"
mv viash "$HOME/.local/bin"

curl -fsSL dl.viash.io | bash
mkdir -p "$HOME/.local/bin"
mv viash "$HOME/.local/bin"

Install Viash in Ubuntu (WSL):

curl -fsSL dl.viash.io | bash
mkdir -p "$HOME/.local/bin"
mv viash "$HOME/.local/bin"

Verify that you have Viash version 0.9.0 or higher:

viash -v

Step 5: install Nextflow

curl -s https://get.nextflow.io | bash
mkdir -p "$HOME/.local/bin"
mv nextflow "$HOME/.local/bin"

curl -s https://get.nextflow.io | bash
mkdir -p "$HOME/.local/bin"
mv nextflow "$HOME/.local/bin"

curl -s https://get.nextflow.io | bash
mkdir -p "$HOME/.local/bin"
mv nextflow "$HOME/.local/bin"

curl -s https://get.nextflow.io | bash
mkdir -p "$HOME/.local/bin"
mv nextflow "$HOME/.local/bin"

curl -s https://get.nextflow.io | bash
mkdir -p "$HOME/.local/bin"
mv nextflow "$HOME/.local/bin"

Verify that Nextflow and Docker are working:

nextflow run hello -with-docker

Expected output:

N E X T F L O W  ~  version 22.10.4
Launching `https://github.com/nextflow-io/hello` [compassionate_keller] DSL2 - revision: 4eab81bd42 [master]
executor >  local (4)
[d5/78e7a6] process > sayHello (2) [100%] 4 of 4 ✔
Bonjour world!
Hello world!
Hola world!
Ciao world!

Optional: install VS Code

It is recommended to install VS Code as it has extensions that help with developing Viash components.

YAML extension (recommended)

The YAML extension provides YAML validation, syntax highlighting, auto-completion, and document outlining. The OpenProblems repository ships schemas that are auto-detected by this extension, making it easier to write and edit Viash config files.

You can find more recommended extensions for developing with Viash at the Viash IDE setup guide.