Installation

Step 1

Install Viash

Requirements

Viash is developed in Scala, so you’ll need to install Java 8, OpenJDK 8 or a later version.
You can run the following command to check if you have Java installed:

java -version
Note

Java version “1.8.x” and “8” are the same release.

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

Installing Viash

To install Viash to a bin folder in your current directory, run the following command to download and run the install script:

wget -qO- dl.viash.io | bash; mv viash $HOME/bin

To verify your installation, run the following command:

viash --help

Requirements

Viash is developed in Scala, so you’ll need to install Java 8, OpenJDK 8 or a later version.
You can run the following command to check if you have Java installed:

java -version
Note

Java version “1.8.x” and “8” are the same release.

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

Installing Viash

To install Viash to a bin folder in your current directory, run the following command to download and run the install script:

curl -fsSL dl.viash.io | bash; mv viash $HOME/bin

To verify your installation, run the following command:

viash --help

Requirements

Setting up WSL2

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 Java 8, OpenJDK 8 or a later version. Install the Viash dependencies by executing this command:
sudo apt-get install -y openjdk-12-jdk unzip zip
Note

You can choose to install default-jdk instead of the more explicit openjdk-12-jdk. However, the Nextflow target platform only supports Java version 8 to 12 at this point in time, so keep that in mind.

  1. Install Nextflow.

Installing Viash

To install Viash to a bin folder in your current directory, run the following command to download and run the install script:

wget -qO- dl.viash.io | bash; mv viash $HOME/bin

To verify your installation, run the following command:

viash --help

Step 2

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.