include external library

Elisabeth Frank

• April 29, 2016 06:26

Hi all,

I am trying to develop a plugin that uses an external library, but when running the plugin, the library wont load (see stack trace below).
Where do I have to put the library jar file on the file system and/or where do I have to include the library in the build process of the plugin so Geneious can find it.

So far, I included it in the build.xml classpath and I moved the library jar to ../GeneiousFiles/lib and to .../Geneious/lib, but this did not help.

Thanks for your help!

stack trace:
java.lang.NoClassDefFoundError
at com.biomax.biomaxImporterPlugin.BiomaxImporter.initBioXMSession(BiomaxImporter.java:47)
at com.biomax.biomaxImporterPlugin.BiomaxImporter.performOperation(BiomaxImporter.java:178)
at com.biomatters.geneious.publicapi.plugin.DocumentOperation.performOperation(DocumentOperation.java:459)
at com.biomatters.geneious.publicapi.plugin.DocumentOperation.performOperation(DocumentOperation.java:405)
at com.biomatters.iseek.plugin.operations.p.run(OperationManager.java:453)
at com.biomatters.geneious.common.operations.b.a(OperationsUtilities.java:149)
at com.biomatters.geneious.common.operations.b.a(OperationsUtilities.java:146)
at com.biomatters.geneious.common.operations.a$c.b(OperationsUtilities.java:125)
at com.biomatters.geneious.common.operations.a$b.a(OperationsUtilities.java:146)
at com.biomatters.iseek.plugin.operations.e.a(OperationManager.java:447)
at com.biomatters.iseek.plugin.operations.u.a(OperationPerformer.java:98)
at com.biomatters.iseek.plugin.operations.OperationAction.performAction(OperationAction.java:122)
at com.biomatters.iseek.plugin.operations.OperationAction.access$000(OperationAction.java:29)
at com.biomatters.iseek.plugin.operations.a.run(OperationAction.java:85)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ClassNotFoundException: com.biomax.bioxm.remotecli.BioXMCli
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 15 more

0

• 

  Richard Moir

  • May 01, 2016 22:19

  Usually you would put a jar like that in a "lib" directory alongside your "src" directory. If you are running from an IDE then you will need to add it to the classpath in the project configuration also.

  • Instructions for IntelliJ
  • Instructions for Eclipse

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• 

  Elisabeth Frank

  • May 10, 2016 13:03

  I want to run the plugin from inside Geneious. So no IDE involved.

  I need to know where to put the jar libraries so that they can be found during runtime, not compilation.

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• 

  Richard Moir

  • May 11, 2016 04:25

  Sorry for the misunderstanding.

  You need to build your plugin as a folder which contains your main jar alongside any other required jars. If you have a look at the build.xml files that are included with the sample plugins (we always recommend building new plugins on top of one of the examples), there is commented out code in there along with instructions for building your plugin as a folder. Your jars go where the build.xml mentions "ExtraFiles". If anything is unclear, let me know.

  For existing examples of this, have a look inside the bundledPlugins folder in your Geneious install directory. We have a few folder type plugins that contain additional jars.

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• 

  Elisabeth Frank

  • May 18, 2016 07:33

  Fantastic, that worked perfect! Thanks for your help on this!

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