I am looking for the way to go to include JAVA jar or classes into a Toolshed tool.

I noticed that JARs are gathered in galaxy-dist/tool-data/shared/jars. e.g. below:

java -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"

What I did, I placed the java class next to the tool xml file, and called in the xml file the java class, using a static path (see below).


java -cp *~/galaxy-dist/tools/joatools* BaseCalls3 -l `head -2 $input | tail -1 | wc -c` -o $output_basecalls -q $output_qualities $input

Can I use a GALAXY environment variable to refer to the directory of the tool? If so, then I can share with Toolshed my tool xml and java class file.
Or is there another method I should follow?

Kind regards,


Joachim Jacob, PhD

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)

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