We have a local instance of galaxy at our institution. I've been trying to use several existing wrappers for tools on galaxy right now, for example, bwa_wrapper, cufflinks_wrapper to run bwa, cufflinks through galaxy. I keep seeing the following error:

An error occurred running this job:Could not determine BWA version
The alignment failed.
Error aligning sequence. /bin/sh: bwa: not found

An error occurred running this job:Could not determine cufflinks version
cufflinks -I 300000 -F 0.050000 -j 0.050000 -p 4 -Q 0 -r
Error running cufflinks. /bin/sh: cufflinks: not found

This is despite the server having cufflinks and bwa available. Is there somewhere I need to put these executables? Any config/ini files that I need to update with the location of the executables?

Thanks for any help,

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