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 <nate@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/