Originally posted by zorph
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[2014-09-17 11:33:06] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Error: Bowtie not found on this system.
However, my issue was that the HPC admin had updated (the default version of) bowtie to a version that wasn't compatible with the installed version of tophat.
I fixed this my removing that module and loading the old one (i.e. changing which version of bowtie was referred to on my path).
http://ccb.jhu.edu/software/tophat/index.shtml lists which version of bowtie is compatible with which version of tophat.
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