FAQ and troubleshooting

Frequently asked questions

How can I add an external resource to my Viash component?

You can add additional resources such as a file containing helper functions. List those files under the resources section of your component config and refer to them in your script using meta["resources_dir"] + "/myresource.txt". See the Viash documentation for concrete examples on how to add helper functions and other resources to your component.

What does __merge__ do?

The __merge__ field merges another YAML file into a Viash config. One of its primary uses is ensuring that all components in a task share the same API.

Each task in OpenProblems contains strict definitions of the input/output file interface of its components and the file formats of those files. These interfaces are stored as YAML files in the api subdirectory of each task. When a component config includes __merge__: ../../api/comp_method.yaml, Viash automatically imports those argument definitions, keeping all method configs consistent with the task’s API.

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Troubleshooting

Choosing between multiple versions of Java

Your system might have multiple versions of Java installed. To check which versions are available (usually under /usr/lib/jvm/):

ls -1 /usr/lib/jvm/

java-11-openjdk
java-19-openjdk
java-19-openjdk-19.0.0.0.36-2.rolling.el8.x86_64
...

Add the following to your ~/.bashrc (or your execution script) to select the correct version:

export JAVA_HOME=/usr/lib/jvm/java-19-openjdk

Permission error with Docker

If you get a permission denied error on Linux, add your user to the docker group:

sudo usermod -aG docker $USER

Log out and back in again, then verify:

groups
docker run hello-world

Docker daemon is not running

If Docker commands fail with a “daemon not running” error, enable Docker to start on boot:

sudo systemctl enable docker
sudo systemctl start docker
docker run hello-world

Viash: command not found

Check whether Viash is installed in $HOME/.local/bin:

ls $HOME/.local/bin/viash

If it exists but the command is still not found, $HOME/.local/bin is likely missing from your PATH. Check with:

echo $PATH

If /home/youruser/.local/bin is absent, look up instructions for adding a folder to your PATH for your operating system and shell.

Nextflow: command not found

Same as above — check $HOME/.local/bin/nextflow exists, then verify $HOME/.local/bin is in your PATH.