Hi

I've set-up a local Galaxy instance and have been using the data manager / tool-shed to set up tools and indexes etc.

I've installed both bowtie2 and tophat2 but when i come to run tophat 2 I get the following error:

tophat2 --num-threads ${GALAXY_SLOTS:-4} /export/system0/home/galaxy/galaxy-dist/tool-data/mm9/bowtie2_index/mm9/mm9,/export/system0/home/galaxy/galaxy-dist/tool-data/mm9/bowtie2_index/mm9/mm9 "/export/system0/home/galaxy/galaxy-dist/database/files/000/dataset_14.dat"

[2015-07-01 16:22:24] Beginning TopHat run (v2.0.9) ----------------------------------------------- [2015-07-01 16:22:24] Checking for Bowtie Bowtie 2 not found, checking for older version.. Error: Bowtie not found on this system.

Clearly there is an issue here with tophat2 knowing where bowtie2 is. What I can fathom is where this is assigned and how to get this working.

In my tool_dependency_dir/bowtie2 there are both 2.2.4 and 2.2.5 packages - this has confused me a bit, but i think it was because the 2.2.5 is a dependency of tophat2 and 2.2.4 a dependency of bowtie2.

Thanks in advance for any insight and help - I suspect it's something trivial as i'm quite new to Galaxy.

-- Simon D. Harding, PhD. MRC HGU MRC IGMM at University of Edinburgh Crewe Road, EDINBURGH, EH4 2XU