Installation

Step 1

Install Requirements

Viash is developed in Scala, so you’ll need to install a Java SE platform, either from Oracle, or OpenJDK. The minimum required version is Java 11, but we recommend Java 17 or 21 (all of these are Long Time Support versions).

You can run the following command to check if you have Java installed:

java -version

To install Java, we encourage to use your distribution’s package manager;

# for Debian/Ubuntu
sudo apt-get update
sudo apt-get install openjdk-17-jdk
# for RHEL/Fedora
sudo yum install java-17-openjdk-devel
# for Arch
sudo pacman -Syy jdk17-openjdk

To get the most out of Viash, you’ll also need to install Docker and Nextflow.

Tip

If you get an error Docker daemon does not seem to be running when executing a docker container, you may need to run sudo systemctl start docker --now to start the docker service. To add the current user to the docker group, run sudo usermod -aG docker $USER and re-login to apply the change.

Viash is developed in Scala, so you’ll need to install a Java SE platform, either from Oracle, or OpenJDK. The minimum required version is Java 11, but we recommend Java 17 or 21 (all of these are Long Time Support versions).

You can run the following command to check if you have Java installed:

java -version

To install Java, first install Homebrew:

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

Next install Java 17 by running:

brew install openjdk@17
Tip

Note that brew may call out that you may want to create a symlink or adjust your PATH. Please take the appropriate steps as is suitable for your case.

To get the most out of Viash, you’ll also need to install Docker and Nextflow.

Viash doesn’t support Windows natively, but Windows Subsystem for Linux 2 can be used instead. Follow the instructions below to get everything ready to use Viash:

  1. Install WSL2 by following the instructions provided by Microsoft. This will install the default distro, Ubuntu.
  2. Follow these instructions provided by Docker to install Docker Desktop with a WSL2 backend. This allows you to run Linux docker containers natively.
  3. Open Ubuntu from the Start menu to start up WSL2.
  4. Run the following command in the Ubuntu terminal to upgrade Ubuntu and its packages to the newest version:
sudo apt-get update && sudo apt-get upgrade -y
  1. Run this command to check if docker is working correctly:
docker run hello-world

If this doesn’t work, read the Docker WSL2 instructions again, you might have missed a step or forgot to reboot your system.

  1. Viash is developed in Scala, so you’ll need to install a Java SE platform, either from Oracle, or OpenJDK. The minimum required version is Java 11, but we recommend Java 17 or 21 (all of these are Long Time Support versions).

Install the Viash dependencies by executing this command:

sudo apt-get install -y openjdk-17-jdk unzip zip
Note

You can choose to install default-jdk instead of the more explicit openjdk-17-jdk.

  1. Install Nextflow.

Step 2

Install Viash

To install Viash to a bin folder on your PATH, run the following command to download and run the install script:

wget -qO- dl.viash.io | bash
sudo mv viash /usr/local/bin

To verify your installation, run the following command:

viash --help

Viash can be easily installed in the working directory by running the following command:

curl -fsSL dl.viash.io | bash

This will download the Viash binary to the current working directory and make it executable.

Next, the Viash executable can be moved to either a system location (/usr/local/bin) or a user location (~/bin):

  1. To install the Viash executable to /usr/local/bin, simply run:

    sudo mv viash /usr/local/bin

    Please note that sudo rights are required.

  2. To install Viash to the $HOME/bin folder, run the following command instead:

    mv viash $HOME/bin/viash

    Make sure to create the ~/bin directory if it doesn’t exist yet and add ~/bin to the $PATH environment variable in your shell.

To verify your installation, run the following command:

viash --help

To install Viash to a bin folder on your PATH, run the following command to download and run the install script:

wget -qO- dl.viash.io | bash
sudo mv viash /usr/local/bin

To verify your installation, run the following command:

viash --help

Step 3

Use the Quickstart

The Quickstart will guide you through the process of creating a Viash component, generating a Nextflow module and incorporating that into a new pipeline.