Hi, I actually fixed it. I changed the wrapper in the line 105 from: cmd_index = 'bowtie-build %s -f %s %s' % ( space, options.own_file, index_path )
to cmd_index = 'bowtie2-build %s -f %s %s' % ( space, options.own_file, index_path ) Luciano On Tue, Jun 19, 2012 at 3:03 PM, Luciano Cosme <cosme.sim...@gmail.com>wrote: > > Hi, > I installed bowtie2 and when running tophat I get the following error: > > Error in tophat: > > [2012-06-19 14:02:39] Beginning TopHat run (v2.0.3) > ----------------------------------------------- > [2012-06-19 14:02:39] Checking for Bowtie > Bowtie version: 2.0.0.6 > [2012-06-19 14:02:39] Checking for Samtools > Samtools version: 0.1.18.0 > [2012-06-19 14:02:39] Checking for Bowtie index files > Error: Could not find Bowtie 2 index files > (/tmp/tmpojo7bV/AgamP3.14.dna.toplevel.*.bt2) > > > > I was wondering if I can create the index files using bowtie2 via command > line and then change the universe_wsgi.ini to: > # Temporary files are stored in this directory. > new_file_path = database/tmp > > > and put the index files there. Anyway, why is it not creating the indexes? > I created links to all bowtie2 executable files. If I remove bowtie 0.12.8, > then I get a error from tophat (bowtie not installed). Is it creating the > index with bowtie 0.12.8? > Thank you. > > Luciano > -- *Luciano Cosme* --------------------------------------------- PhD Candidate Texas A&M Entomology Vector Biology Research Group www.lcosme.com 979 845 1885 co...@tamu.edu ---------------------------------------------
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