Hello, 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). e.g. <command> java -cp *~/galaxy-dist/tools/joatools* BaseCalls3 -l `head -2 $input | tail -1 | wc -c` -o $output_basecalls -q $output_qualities $input </command> 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 -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib