[Biojava-l] Set-up on True64

[Warth,Rainer,LAUSANNE,NRC/BS]

Dear all, 
   I am new to biojava. I am currently setting it up on a Compaq True 64
v.5.1 server.
I managed to get things going on my Windows and Linux box ( although this
was not very hard). Now I encounter this problem in the Compa machine and I
do not really know what 
to do.

Best, Rainer

I did set up the enviroment:   =========================================

LSBioIT1.crn.nestrd.ch> setenv CLASSPATH
/home/RWa/bin/biojava-1.22.jar:/home/RWa/bin/xerces.jar:/home/RWa/bin/byteco
de-0.91.jar:.


First I tried :  ========================================================

LSBioIT1.crn.nestrd.ch> ls
AL121903.embl            SimpleAssemblyTest.java  TestGenbank.java
TestTranslation.java
AL121903.genbank         TestEmbl.class           TestRefSeqPrt.java
db
CVS                      TestEmbl.java            TestSubSequence.java
utrs.fa
GCContent.java           TestEmbl2.java           TestSwissprot.java
LSBioIT1.crn.nestrd.ch> pwd
/home/RWa/F_computer/java_src/biojava-live/demos/seq
LSBioIT1.crn.nestrd.ch> java3 TestEmbl AL121903.embl
java.lang.NoClassDefFoundError: TestEmbl: TestEmbl (wrong name:
seq/TestEmbl)
        at java.lang.ClassLoader.defineClass0 (ClassLoader.java)
        at
java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.secur
ity.ProtectionDomain) (ClassLoader.java:498) (pc 87)
        at java.security.SecureClassLoader.defineClass
(SecureClassLoader.java:111) (pc 27)
        at java.net.URLClassLoader.defineClass (URLClassLoader.java:248) (pc
171)
        at java.net.URLClassLoader.access$100 (URLClassLoader.java:56) (pc
3)
        at java.net.URLClassLoader$1.run (URLClassLoader.java:195) (pc 43)
        at
java.security.AccessController.doPrivileged(java.security.PrivilegedExceptio
nAction,java.security.AccessControlContext) (AccessController.java)
        at java.net.URLClassLoader.findClass (URLClassLoader.java:188) (pc
13)
        at java.lang.ClassLoader.loadClass(java.lang.String,boolean)
(ClassLoader.java:309) (pc 43)
        at sun.misc.Launcher$AppClassLoader.loadClass (Launcher.java:286)
(pc 36)
        at java.lang.ClassLoader.loadClass(java.lang.String)
(ClassLoader.java:265) (pc 3)
LSBioIT1.crn.nestrd.ch>



Then I tried:
===============================================================


LSBioIT1.crn.nestrd.ch> pwd
/home/RWa/F-computer/java_src/biojava-live/demos

LSBioIT1.crn.nestrd.ch> java3 seq/TestEmbl seq/AL121903.embl
java.lang.AbstractMethodError:
org.biojava.bio.symbol.Alphabet.getAlphabets()
        at org.biojava.bio.symbol.AbstractAlphabet.getGapSymbol
(AbstractAlphabet.java:235) (pc 1)
        at org.biojava.bio.symbol.AbstractAlphabet.getAmbiguity
(AbstractAlphabet.java:99) (pc 10)
        at
org.biojava.bio.symbol.AlphabetManager.characterTokenizationFromXML
(AlphabetManager.java:929) (pc 187)
        at org.biojava.bio.symbol.AlphabetManager.alphabetFromXML
(AlphabetManager.java:889) (pc 318)
        at org.biojava.bio.symbol.AlphabetManager.<clinit>
(AlphabetManager.java:720) (pc 429)
        at org.biojava.bio.seq.DNATools.<clinit> (DNATools.java:52) (pc 2)
rethrown as org.biojava.bio.BioError: Unable to initialize DNATools
        at org.biojava.bio.seq.DNATools.<clinit> (DNATools.java:83) (pc 279)
        at seq.TestEmbl.main             (TestEmbl.java:22)      (pc 70)
LSBioIT1.crn.nestrd.ch>

---
Dr. Rainer Warth
Research Scientist Bioinformatics

Nestle Research Center
NESTEC LTD.
Vers-Chez-LES-BLANC	phone: 	+41/21 785 87 13
1000 LAUSANNE 26	FAX:	+41/21 785 89 25
SWITZERLAND		e-mail:	rainer.warth@rdls.nestle.com