Requirements

A list of required software to start contributing to OpenProblems

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 these tools installed, feel free to skip this boring page and go to the respective page on what you want to do either Create component or Create a new task.

Step 1: install Bash

Debian/Ubuntu

Bash is already included in most Debian- and Ubuntu-based distributions. However, if for some reason it’s not installed, open a terminal and run the following commands:

sudo apt-get update
sudo apt-get install bash

RHEL/Fedora

Bash is already included in most RHEL- and Fedora-based distributions. However, if for some reason it’s not installed, open a terminal and run the following commands:

sudo yum install bash

Arch

Bash is already included in most Arch-based distributions. However, if for some reason it’s not installed, open a terminal and run the following commands:

sudo pacman -S bash

macOS

Bash is already included in macOS.

Windows

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”. Enter the following command to enable the features necessary to run WSL and install the Ubuntu distribution of Linux.

wsl --install

After rebooting the system, open Ubuntu by visiting the Windows Start menu or by entering the ubuntu command in PowerShell or Windows Command Prompt. Since Bash is already included in Ubuntu, no further actions are needed.

Content adapted from the WSL installation instructions

Verify that you have Bash version 3.2 or higher.

bash --version

Output

GNU bash, version 5.1.16(1)-release (x86_64-pc-linux-gnu)
Copyright (C) 2020 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>

This is free software; you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Step 2: install Java

You will need Oracle Java >=11 or OpenJDK >=11 to be installed.

Debian/Ubuntu

Run the following commands:

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

RHEL/Fedora

Run the following command:

sudo yum install java-11-openjdk-devel

Arch

Run the following command:

sudo pacman -S jdk11-openjdk

macOS

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

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

Next, install Java 11 by running:

brew install openjdk@11

Windows

Open Ubuntu in WSL and run the following commands:

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

Verify that you have Java version 11 or higher.

java -version

Output

openjdk 11.0.24 2024-07-16
OpenJDK Runtime Environment Temurin-11.0.24+8 (build 11.0.24+8)
OpenJDK 64-Bit Server VM Temurin-11.0.24+8 (build 11.0.24+8, mixed mode)

Step 3: install Docker

Debian/Ubuntu

Update package index by running:

sudo apt update

Install Docker by running:

sudo apt install docker.io

Enable the Docker service automatically at boot by running:

sudo systemctl enable docker

Add the current user to the Docker group by running:

sudo usermod -aG docker $USER

RHEL/Fedora

On RHEL, run the following commands:

sudo yum install -y yum-utils
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

On Fedora, run the following commands:

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

Enable the Docker service automatically at boot by running:

sudo systemctl enable docker

Add the current user to the Docker group by running:

sudo usermod -aG docker $USER

Arch

Install Docker by running:

sudo pacman -S docker

Enable the Docker service automatically at boot by running:

sudo systemctl enable docker

Add the current user to the Docker group by running:

sudo usermod -aG docker $USER

macOS

Download and install Docker Desktop for Mac and download Docker Desktop for Mac.

Windows

Open Ubuntu in WSL and follow the following instructions.

Update package index by running:

sudo apt update

Install Docker by running:

sudo apt install docker.io

Enable the Docker service automatically at boot by running:

sudo systemctl enable docker

Add the current user to the Docker group by running:

sudo usermod -aG docker $USER

Verify that Docker is working by running:

docker run hello-world

Output

Unable to find image 'hello-world:latest' locally
latest: Pulling from library/hello-world
c1ec31eb5944: Pulling fs layer
c1ec31eb5944: Verifying Checksum
c1ec31eb5944: Download complete
c1ec31eb5944: Pull complete
Digest: sha256:91fb4b041da273d5a3273b6d587d62d518300a6ad268b28628f74997b93171b2
Status: Downloaded newer image for hello-world:latest

Hello from Docker!
This message shows that your installation appears to be working correctly.

To generate this message, Docker took the following steps:
 1. The Docker client contacted the Docker daemon.
 2. The Docker daemon pulled the "hello-world" image from the Docker Hub.
    (amd64)
 3. The Docker daemon created a new container from that image which runs the
    executable that produces the output you are currently reading.
 4. The Docker daemon streamed that output to the Docker client, which sent it
    to your terminal.

To try something more ambitious, you can run an Ubuntu container with:
 $ docker run -it ubuntu bash

Share images, automate workflows, and more with a free Docker ID:
 https://hub.docker.com/

For more examples and ideas, visit:
 https://docs.docker.com/get-started/

Step 4: install Viash

Debian/Ubuntu

Install Viash by running:

curl -fsSL dl.viash.io | bash

mkdir -p "$HOME/.local/bin"

mv viash "$HOME/.local/bin"

Tip: Make sure that the $HOME/.local/bin folder is in your $PATH variable.

RHEL/Fedora

Install Viash by running:

curl -fsSL dl.viash.io | bash

mkdir -p "$HOME/.local/bin"

mv viash "$HOME/.local/bin"

Tip: Make sure that the $HOME/.local/bin folder is in your $PATH variable.

Arch

Install Viash by running:

curl -fsSL dl.viash.io | bash

mkdir -p "$HOME/.local/bin"

mv viash "$HOME/.local/bin"

Tip: Make sure that the $HOME/.local/bin folder is in your $PATH variable.

macOS

Install Viash by running:

curl -fsSL dl.viash.io | bash

mkdir -p "$HOME/.local/bin"

mv viash "$HOME/.local/bin"

Tip: Make sure that the $HOME/.local/bin folder is in your $PATH variable.

Windows

Install Viash in Ubuntu by running:

curl -fsSL dl.viash.io | bash

mkdir -p "$HOME/.local/bin"

mv viash "$HOME/.local/bin"

Tip: Make sure that the $HOME/.local/bin folder is in your $PATH variable.

Verify that you have Viash version 0.6.7 or higher.

viash -v

Output

viash 0.9.0 (c) 2020 Data Intuitive

Step 5: install Nextflow

Debian/Ubuntu

Install Nextflow by running:

curl -s https://get.nextflow.io | bash

mkdir -p "$HOME/.local/bin"

mv nextflow "$HOME/.local/bin"

RHEL/Fedora

Install Nextflow by running:

curl -s https://get.nextflow.io | bash

mkdir -p "$HOME/.local/bin"

mv nextflow "$HOME/.local/bin"

Arch

Install Nextflow by running:

curl -s https://get.nextflow.io | bash

mkdir -p "$HOME/.local/bin"

mv nextflow "$HOME/.local/bin"

macOS

Install Nextflow by running:

curl -s https://get.nextflow.io | bash

mkdir -p "$HOME/.local/bin"

mv nextflow "$HOME/.local/bin"

Windows

Install Nextflow by running:

curl -s https://get.nextflow.io | bash

mkdir -p "$HOME/.local/bin"

mv nextflow "$HOME/.local/bin"

Verify that Nextflow and Docker are working by running:

nextflow run hello -with-docker

N E X T F L O W  $HOME  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 and use VS Code as this will help with the development of components due to the use of extensions and YAML schemas.

VS code can be downloaded from this page.

There are installers available for all major operating systems, so simply download and install the version for your system.

YAML extension (recommended)

This extension provides YAML validation, syntax highlighting, auto completion and document outlining for YAML. A must have for writing and editing Viash config files!

The OpenProblems repo has schemas that help with writing the API and Viash config files. The extension auto detects these schemas.

You can find more recommended extensions for developing with Viash by visiting following link.