On Tue, Apr 17, 2012 at 1:00 PM, JIE CHEN <jiechenable1...@gmail.com> wrote:
> Thank you Nate. Your advise is very helpful to me. I installed the > binaries like you said. Right now the binaries can be run successfully in > the command line prompt. However i run into other problems : > > Failed to open input file: > /usr/local/projects/galaxy-dist/tool-data/taxonomy/names.dmp > > > What i have done: > 1. downloaded the .tar.gz file from the link you told me > 2. tar zxvf name.tar.gz > 3. then i found the three executables which are: taxBuilder, taxonomy2tree > and tree2PS-fast. > 4. made symbolic link of these files to the /usr/local/bin > > what else shall i do? Thanks. > > Tyler > > On Tue, Apr 17, 2012 at 10:36 AM, Nate Coraor <n...@bx.psu.edu> wrote: > >> On Apr 17, 2012, at 1:32 PM, JIE CHEN wrote: >> >> > Dear all, >> > >> > I was trying to run the build-in function "Fetch taxonomic >> representation" on my local instance of Galaxy, however it doesn't work as >> I expect. >> > The error message is: >> > /bin/sh: taxBuilder: not found >> > >> > >> > Anyone has seen this problem before? Please tell me what to do to solve >> this problem? A lot of thanks >> >> Hi Tyler, >> >> Some Galaxy tools depend on external binaries not included in the Galaxy >> distribution, and this is one of those tools. The full list and where to >> get the tools from can be found here: >> >> http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies >> >> This specific tool can be found at: >> >> https://bitbucket.org/natefoo/taxonomy >> >> --nate >> >> > >> > Tyler >> > ___________________________________________________________ >> > 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/ >> >> >
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