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From sudha sadhasivam <sudhasadhasi...@yahoo.com>
Subject Hadoop + Biojava - error
Date Thu, 31 Jul 2008 09:59:40 GMT
Respected Sir
We are ME students working on Hadoop for bioinformatics. 
We have installed Hadoop on Linux and it is working well. 
We have installed biojava (an extension of java for bioinformatics) for DNA sequence searching.
To install biojava, we have to copy the jar files biojava-live.jar, commons-cli.jar, bytecode.jar,
commons-collections-2.1.jar, commons-pool-1.1.jar in /root/usr/java/jdk1.6.0_06/jre/lib/ext
Examples in biojava works well.
Now if we run hadoop dfs after installation of biojava the following error is displayed
[root@oss8 hadoop-0.17.0]# bin/hadoop dfs -put conf input
Exception in thread "main" java.lang.NoSuchMethodError: org.apache.commons.cli.OptionBuilder.withArgPattern(Ljava/lang/String;I)Lorg/apache/commons/cli/OptionBuilder;
        at org.apache.hadoop.util.GenericOptionsParser.buildGeneralOptions(GenericOptionsParser.java:164)
        at org.apache.hadoop.util.GenericOptionsParser.parseGeneralOptions(GenericOptionsParser.java:213)
        at org.apache.hadoop.util.GenericOptionsParser.<init>(GenericOptionsParser.java:120)
        at org.apache.hadoop.util.GenericOptionsParser.<init>(GenericOptionsParser.java:105)
        at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:59)
        at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:79)
        at org.apache.hadoop.fs.FsShell.main(FsShell.java:1866)
If we remove commons-cli.jar (jar file for bio java)  from /root/usr/java/jdk1.6.0_06/jre/lib/ext
directory then hadoop examples work.
We think that both hadoop and commons-cli.jar files have org.apache in common.
As we want to run biojava in hadoop DFS, can you suggest a way to correct this error?
Please reply at the earliest. Thanking you
With regards
Geetha Jini, Komagal Meenakshi

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