Re: [galaxy-dev] Tools accessing web services
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 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 > > ___ > 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/ > ___ 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/
Re: [galaxy-dev] Tools accessing web services
Can anyone answer this, please, or point me to the relevant documentation? On 07/11/2011, Amelia Ireland 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 ___ 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/
[galaxy-dev] 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 ___ 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/
