Hello.
I'm trying to use msBID on some mzXML and pepXML files but I continue
to get problems.
I'm only interested in getting the program to run past the first step
at this juncture.
This is what I've done:
1. placed peakID.param in folder with mzXML files and pepXML files
2. export CLASSPATH=".:./jars/colt.jar:./jars/msBID.jar:./jars/
concurrent.jar:./jars/jrap.jar"
3. echo $CLASSPATH ## to verify that CLASSPATH has been set
4. java -Xmx2g org.systemsbiology.msanalyzer.scan.FeatureExtractor
mzXML_file > mzXML_file.out
At this point I get this error:
Exception in thread "main" java.lang.NoClassDefFoundError: org/
systemsbiology/msanalyzer/scan/FeatureExtractor
Caused by: java.lang.ClassNotFoundException:
org.systemsbiology.msanalyzer.scan.FeatureExtractor
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:
org.systemsbiology.msanalyzer.scan.FeatureExtractor. Program will
exit.
I'm running this on a RHEL 5.4 (64bit) computer with SUN Java 1.6.0_21
(64bit).
Any suggestions on what's wrong?
Thanks in advance.
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