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Has this issue been resolved? Any updates? I'm dealing the exact same errors/error logs as described above.
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Unfortunately no. Your only option is to use TopHat 2.0.9 on OS X, unless you want to try compiling from source (not simple).Comment
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Ok. Thank you. I'll continue with v.2.0.9 then. I'm still waiting for a response from the developers after I reported the issue. Once I get an update I will post it here.Comment
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Weird. After I replaced Tophat's 2.0.12 version with the 2.0.9 version it doesn't find bowtie anymore. Even though it's in the PATH. I tried with --bowtie1 and --bowtie2. Bowtie2 is present as I can access it from the command line.
What's the catch?
[2014-08-27 09:09:09] Beginning TopHat run (v2.0.9)
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[2014-08-27 09:09:09] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Error: Bowtie not found on this system.Comment
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You may need a corresponding older version of bowtie to go with TopHat 2.0.9. Try v.2.1.0.Comment
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Thank's. That worked.Comment
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