Hello,
I'm still trying to get through the 2.1 getting started document
(http://base.thep.lu.se/chrome/site/doc/user/getting_started.html). Moving on
to section 2d, "Analysing an experiment step I". I'm getting an error when I
try to run the RMAExpress plug-in job. The stack trace is below. I'm curious
as to why the plug-in is looking for the RMAExpressConsole application in the
Tomcat temp directory. I think I've configured everything properly so far.
The RMAExpressConsole application file is located in the same directory as the
plug-in's affymetrix.jar library.
By the way, if a job fails, it would be nice to see that reported on the
"Properties" tab of the "View job" panel. Also, if this all works out, I've
got about 100 raw .CEL files to load. How's the batch import functionality
coming along? Would it be possible to use the BASE Java API to load the files
myself? Another thing - all the files have the extension in uppercase, meaning
that the default %.cel search string doesn't find them.
Thanks,
Jesse
java.io.IOException: Cannot run program "RMAExpressConsole" (in
directory "C:\Program Files\Apache Software Foundation\Tomcat
6.0\temp\RMAExpress plug-in\905"): CreateProcess error=2, The system
cannot find the file specified
at java.lang.ProcessBuilder.start(Unknown Source)
at java.lang.Runtime.exec(Unknown Source)
at java.lang.Runtime.exec(Unknown Source)
at se.lu.thep.affymetrix.RMAExpress.runBinary(RMAExpress.java:150)
at
se.lu.thep.affymetrix.AbstractExternalBinaryPlugin.run(AbstractExternalBinaryPlugin.java:262)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:89)
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:421)
at java.lang.Thread.run(Unknown Source)
Caused by: java.io.IOException: CreateProcess error=2, The system cannot find
the file specified
at java.lang.ProcessImpl.create(Native Method)
at java.lang.ProcessImpl.<init>(Unknown Source)
at java.lang.ProcessImpl.start(Unknown Source)
... 8 more
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