How To Get Picard-1.33 Working

Question

[Biomed]

I downloaded Picard-1.33 and I can't seem to get it working under a unix command line. Any help in how you should start this program with help option?

Exception in thread "main" java.lang.NoClassDefFoundError: picard-1/33/jar
Caused by: java.lang.ClassNotFoundException: picard-1.33.jar
        at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
Could not find the main class: picard-1.33.jar.  Program will exit.

Answer 1

[Pierre Lindenbaum]

The file picard-1.33.jar is just a library.

Go into the directory picard-tools-1.33 and run the tool with the jar option:

java -jar NormalizeFasta.jar

If needed, set the CLASSPATH for example, under unix that would be something like

export CLASSPATH=/path/to/picard-1.33.jar:/path/to/sam-1.33.jar

[Biomed]

I need to learn more java :) It worked. Thanks