Tools accessing web services
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
Can anyone answer this, please, or point me to the relevant documentation? On 07/11/2011, Amelia Ireland <aireland@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
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 <aireland@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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participants (2)
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Amelia Ireland -
Daniel Blankenberg