Troubleshooting
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-openjdkIn 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-openjdkPermission 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 $USERAfter 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.
groupsyouruser wheel dockerdocker run hello-worldHello 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-worldHello 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/sbinIf /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/sbinIf /home/youruser/.local/bin is not there, look up instructions on how to add a folder to your PATH variable for your operating system.