Hi Amelia,

Sorry for the delay in reply.  Could you provide a copy of your xml file and we 
can take a look.


Thanks for using Galaxy,

Dan


On Nov 21, 2011, at 12:26 PM, Amelia Ireland wrote:

> Can anyone answer this, please, or point me to the relevant documentation?
> 
> On 07/11/2011, Amelia Ireland <airel...@lbl.gov> wrote:
>> Apologies in advance for the newbie question.
>> 
>> I have a script that uses various UniProt web services. The script
>> sends off a request to the UniProt server, waits for it to be
>> returned, and then writes the results to a file. This works fine as a
>> standalone script, but when plugged into Galaxy, I get this error:
>> 
>> ⇝ KeyError: 'GALAXY_URL'
>> URL: http://127.0.0.1:8080/tool_runner/index
>> 
>> Does Galaxy "intervene" in the operation of all tools that access
>> outside web services, and if so, do I need to rewrite the tool as one
>> that acts as a data source (like the UCSC browser, biomart, etc.)? The
>> data sources documentation did not mention whether this was necessary
>> or not.
>> 
>> Thanks!
>> 
>> --
>> Amelia Ireland
>> Scientific Curator, Gene Ontology project
>> http://www.berkeleybop.org || http://www.geneontology.org
>> Preventing Euthanasia Through Rescue: http://petrescueinc.org
>> 
> 
> 
> -- 
> Amelia Ireland
> Scientific Curator, Gene Ontology project
> http://www.berkeleybop.org || http://www.geneontology.org
> Preventing Euthanasia Through Rescue: http://petrescueinc.org
> 
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