Troubleshooting

Discover how to troubleshoot common issues.

Choosing between multiple versions of Java

Your system might have multiple versions of Java installed. First determine which versions of Java are installed. This directory can usually be found at /usr/lib/jvm/. Example:

$ ls -1 /usr/lib/jvm/
java
java-11
java-11-openjdk
java-11-openjdk-11.0.17.0.8-2.el8_6.x86_64
java-1.8.0
java-1.8.0-openjdk
java-1.8.0-openjdk-1.8.0.352.b08-2.el8_6.x86_64
java-19
java-19-openjdk
java-19-openjdk-19.0.0.0.36-2.rolling.el8.x86_64
java-openjdk
jre
jre-11
jre-11-openjdk
jre-11-openjdk-11.0.17.0.8-2.el8_6.x86_64
jre-1.8.0
jre-1.8.0-openjdk
jre-1.8.0-openjdk-1.8.0.352.b08-2.el8_6.x86_64
jre-19
jre-19-openjdk
jre-19-openjdk-19.0.0.0.36-2.rolling.el8.x86_64
jre-openjdk

In the example above, it would be recommended to include the following command as part of your execution script or in your ~/.bashrc:

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

Permission error with Docker

If you get a permission denied error on a Linux system, you may need to add your user to the docker group.

sudo usermod -aG docker $USER

After running the command above, you will need to log out and back in again. After doing so, run the following commands to verify that everything is working.

groups
youruser wheel docker
docker run hello-world
Hello from Docker!
This message shows that your installation appears to be working correctly.
...

Docker error – the docker daemon is not running

If you get the error above, the Docker daemon may not have been started yet.

Figure out how to enable your system to launch Docker on boot. For example, on

sudo systemctl enable docker
docker run hello-world
Hello from Docker!
This message shows that your installation appears to be working correctly.
...

Viash: command not found

Check whether Viash was indeed installed in your $HOME/.local/bin folder by running:

ls $HOME/.local/bin/viash

/home/youruser/.local/bin/viash

If it was, then the $HOME/.local/bin folder is likely not in your PATH variable. Run the following command to check whether it’s missing from your PATH variable:

echo $PATH
/home/youruser/.local/bin:/home/youruser/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin

If /home/youruser/.local/bin is not there, look up instructions on how to add a folder to your PATH variable for your operating system.

Nextflow: command not found

Check whether Nextflow was indeed installed in your $HOME/.local/bin folder by running:

ls $HOME/.local/bin/nextflow

/home/youruser/.local/bin/nextflow

If it was, then the $HOME/.local/bin folder is likely not in your PATH variable. Run the following command to check whether it’s missing from your PATH variable:

echo $PATH
/home/youruser/.local/bin:/home/youruser/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin

If /home/youruser/.local/bin is not there, look up instructions on how to add a folder to your PATH variable for your operating system.