On Sat, Aug 30, 2014 at 11:17 AM, Melissa Cline <cl...@soe.ucsc.edu> wrote:
> Hi folks,
>
> I'm attempting something that should be straightforward, but it's not.  I
> have a tool that runs a JAR file, which I have bundled with the tool.  I
> simply want to run the JAR file.  And to paraphrase Thomas Edison, I've
> tried several thousand things that do not work (at least for me), from
> setting the JAVA_JAR_PATH environment variable in the tool_dependencies.xml
> file to trying to copy the JAR file into the tool-data/shared/jars
> subdirectories (which is the closest thing I've got to working).  So, at
> long last I'm doing the sensible thing and looking for one simple working
> example that I can use as a template.  Who can suggest a good toolshed tool
> (either main or test) that involves running its own JAR file, and that
> works?
>
> Thanks!
>
> Melissa

Here are a couple of my wrappers for Java tools, but I would
suggest you invoke the Java script with an absolute path to the
JAR file:

$ java -jar ...

Here is two examples done via a Python wrapper script (mainly
used for pre or post processing the data files):

https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3
https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go

For EffectiveT3 which is open source and can therefore be easily
redistributed, I set an environment variable EFFECTIVET3 for the
location of the Jar file, which is used to invoke it via Java:

$ java -jar ...

For the Blast2GO wrapper, I require the person installing it setup
an environment variable B2G4PIPE pointing at the folder with
the JAR file. Older versions of this tool you be launched with the
same -jar approach, but the current release requires setting a
class path instead:

$ java -cp ...

I hope that helps, if not there are bound to be other Java examples
in the ToolShed.

Peter
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