Hello guys, I've got a problem with the integration of the BWA Tool in Galaxy. I installed BWA and Galaxy in a virtual box and now I want integrate BWA as a tool. For this I have to do this steps: $ sudo cp /home/ubuntu/galaxy-dist/bwa-0.7.4/bwa /usr/local/bin now bwa can be run from the command line $ bwa The Galaxy tool also requires a loc file which contains the locations of indexes for locally stored genome builds. We don't have any so we can just use the empty sample: $ cp tool-data/bwa_index.loc.sample tool-data/bwa_index.loc $ sh run.sh --reload The problem is, that in my tool-data folder doesn't exist bwa files even if bwa is installed and aso linked in the bin folder! I hope you can help me, because I don't know what to do now! Thanks and greets, Anna