Re: [Useq-users] ChIPSeq java error

[David N. <Dav...@hc...>]

Hello Andrew,

This is easily fixed, it is looking at /usr/bin/java .  I'll just disable
it.  The apps will choke if run on 1.4 and throw an error message so no
need to check.

-cheers, D

On 2/6/12 12:37 PM, "Oler, Andrew (NIH/NIAID) [C]" <and...@ni...>
wrote:

>Hi David,
>
>I'm running the ChIPSeq application from USeq 8.0.7 and I'm getting this
>error:
>
>The following problems were encountered when processing your parameter
>file.  Correct and restart. ->
>Your java application is not >= 1.6 (type 'java -version' on the cmd
>line). Install the most recent java from http://www.java.com/en/download/
>.
>Your save results directory exits, may overwrite the files within.
>
>When I type java -version on the command line, I get this output:
>java -version
>java version "1.6.0_22"
>Java(TM) SE Runtime Environment (build 1.6.0_22-b04)
>Java HotSpot(TM) 64-Bit Server VM (build 17.1-b03, mixed mode)
>
>The java version is fine, so I'm not sure what the problem is.  java is
>an alias for a locally installed version of java, which is 1.6.  Could it
>be that the ChIPSeq program calls '/usr/bin/java' instead of 'java'?
>
>/usr/bin/java -version
>java version "1.4.2"
>gij (GNU libgcj) version 4.1.2 20080704 (Red Hat 4.1.2-46)
>
>Copyright (C) 2006 Free Software Foundation, Inc.
>This is free software; see the source for copying conditions.  There is NO
>warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
>PURPOSE.
>
>I'm running this on a system where I can't change the binaries in
>/usr/bin/.  Any suggestions?
>
>Thanks,
>
>Andrew
>
>Andrew Oler, Ph.D.
>Contractor - Lockheed Martin
>High-Throughput Sequencing Bioinformatics Specialist
>Computational Biology Section
>Bioinformatics and Computational Biosciences Branch (BCBB)
>OCICB/OSMO/OD/NIAID/NIH
>
>31 Center Drive, Room 3B62
>Bethesda, MD 20892
>Mobile: 240-507-3791
>Office: 301-402-5685
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>(Within NIH)
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>
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