Looks like Tophat is choking when trying to parse your Bowtie version. You'll want to verify that a recent version of Bowtie2 (using Tophat2 in Galaxy requires Bowtie2) is installed and is in your Galaxy user's path. Once these requirements are met, you should be able to use Tophat2.
Using Tophat requires Tophat version 1.4.x and a recent version of Bowtie. Best, J. On Dec 27, 2012, at 3:23 PM, Luciano Cosme wrote: > Howdy, > I am getting the following error with tophat: > Error in tophat: > > [2012-12-27 15:08:40] Beginning TopHat run (v2.0.5) > ----------------------------------------------- > [2012-12-27 15:08:40] Checking for Bowtie > Traceback (most recent call last): > File "/usr/bin/tophat", line 4035, in <module> > sys.exit(main()) > File "/usr/bin/tophat", line 3836, in main > check_bowtie(params) > File "/usr/bin/tophat", line 1473, in check_bowtie > bowtie_version = get_bowtie_version(params.bowtie2) > File "/usr/bin/tophat", line 1351, in get_bowtie_version > bowtie_version = [int(x) for x in ver_numbers[:3]] + > [int(ver_numbers[3][4:])] > IndexError: list index out of range > > I tried Tophat and Tophat2 a couple times and always giving me the same > error. The reads I am trying to map are from small RNA sequencing project. I > am trying to map the unannotated reads back to the genome. I am not sure what > is causing this problem, any help will be appreciated. > > Thank you. > > Luciano > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
