I would also recommend getting the latest XML wrappers from here:
  http://hannonlab.cshl.edu/fastx_toolkit/download.html

Or at least changing "zcat" to "cat" in your XML files, as "zcat" on Mac-OS 
behaves differently than linux's (and that is the source of your error message).



Nate Coraor wrote, On 05/11/2011 10:22 AM:
> Owen Hardy wrote:
>> Hi,
>>
>> I set up a local instance on OS 10.6 and was using some fasta tools but 
>> noticed fasta width formatter does not execute. Although it shows in my 
>> local web interface I do not see width formatter in the tools.conf.xml, nor 
>> does the python script appear in /tools/fasta_tools with the others.  I also 
>> browsed source from central and dist in fasta_tools and do not see it there 
>> either...Thanks for any help.
>>
>> An error occurred running this job:/bin/sh: fasta_formatter: command not 
>> found
>> zcat: /Users/Owen/Galaxy/galaxy-dist/database/files/000/dataset_190.dat.Z: 
>> No such file or directory
> 
> Hi Owen,
> 
> Galaxy has various external dependencies for which it provides wrappers
> - this is one of them, namely, the FASTX-Toolkit, available here:
> 
>   http://hannonlab.cshl.edu/fastx_toolkit/
> 
> If you install the Toolkit and insure that it's on your $PATH (i.e. you
> can run 'fasta_formatter' on the command line), using it in Galaxy
> should work.
> 
> --nate
> 
>>
>>
> 
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