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
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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