search

Integrative-Transcriptomics / DamageProfiler

A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage
GNU General Public License v3.0
17 stars 4 forks source link

How to run in Computing Cluster? #60

Open sultandromeda opened 8 months ago

sultandromeda commented 8 months ago

Hi, Thanks for a cool tool

I am struggling to use it in computing clusters I uploaded tar.gz and opened it with the following command:

tar -xzvf v1.1.tar.gz

I tried to use via:

java -Xmx8G -jar /project/lab/sultandromeda/DamageProfiler/DamageProfiler-1.1/jars/DamageProfiler-1.0-java8.jar

and it showed this error: Exception in thread "Thread-0" java.lang.NoClassDefFoundError: javafx/application/Application at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:756) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) at java.net.URLClassLoader.defineClass(URLClassLoader.java:473) at java.net.URLClassLoader.access$100(URLClassLoader.java:74) at java.net.URLClassLoader$1.run(URLClassLoader.java:369) at java.net.URLClassLoader$1.run(URLClassLoader.java:363) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:362) at java.lang.ClassLoader.loadClass(ClassLoader.java:418) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352) at java.lang.ClassLoader.loadClass(ClassLoader.java:351) at RunDamageProfiler.lambda$main$0(RunDamageProfiler.java:23) at java.lang.Thread.run(Thread.java:750) Caused by: java.lang.ClassNotFoundException: javafx.application.Application at java.net.URLClassLoader.findClass(URLClassLoader.java:387) at java.lang.ClassLoader.loadClass(ClassLoader.java:418) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352) at java.lang.ClassLoader.loadClass(ClassLoader.java:351) ... 14 more

This is my first time using this tool, and I quite do not get it how to run. I appreciate your help

JudithNeukamm commented 8 months ago

Hello! It looks like the JavaFX is missing. Have to tried to install it alongside Java? If you are using Ubuntu, you can easily use this command for installing:

sudo apt-get install openjfx

Let me know if this is not working.

sultandromeda commented 7 months ago

Hi Judith,

I used module load java/17, and it worked. Thank you a lot!