I was trying to use a tool a tool written in java called "fastqc" (for people who are interested in what is fastqc. when I tried typing the command :" fastqc" I got the error:
Exception in thread "main" java.lang.NoClassDefFoundError: uk/ac/babraham/FastQC/FastQCApplication Caused by: java.lang.ClassNotFoundException: uk.ac.babraham.FastQC.FastQCApplication at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:323) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:268)
when someone had similar previously,some one suggested that in similar case, I need to set the class path to the directory which contains FastQC installation:
and depending on having a standard class path or non-standard classpath on my machine, I need to append existing classpath like:
java -Xmx250m -classpath /usr/local/FastQC uk.ac.bbsrc.babraham.FastQC.FastQCApplication
java -Xmx250m -classpath /usr/local/FastQC:$CLASSPATH uk.ac.bbsrc.babraham.FastQC.FastQCApplication
Since my directory which contains the FastQC is /u32/myusername/Tool/FastQC
so I tried both:
java -Xmx250m -classpath /u32/myusername/Tool/FastQC uk.ac.bbsrc.babraham.FastQC.FastQCApplication
java -Xmx250m -classpath /u32/myusername/Tool/FastQC:$CLASSPATH uk.ac.bbsrc.babraham.FastQC.FastQCApplication
but none of them seemed to work.
Did I mess something up? I am not sure about what
-Xmx250m means, with or without it, the path setting did not work.
Sorry for my ignorance. Any idea or suggestion appreciated.