Error running workflow via API
The API interface is translating my parameters into python repr strings instead of actual strings. A command that should look like this: createPrimerFile.py /minilims/galaxy-data/primerTemplates/nextera.2x.primers.fasta NNNNNN NNNNNN > /slipstream/galaxy/production/data/files/020/dataset_20664.dat is getting run as this: createPrimerFile.py /minilims/galaxy-data/primerTemplates/nextera.2x.primers.fasta __lt__galaxy.tools.parameters.basic.RuntimeValue object at 0x792be10__gt__ NNNNNN > /slipstream/galaxy/production/data/files/020/dataset_20728.dat The input table in the tool info page is: Input Parameter Value Note for rerun chemistry type: <galaxy.tools.parameters.basic.RuntimeValue object at 0x7fee4425ca10> First barcode NNNNNN Second (optional) barcode NNNNNN I’m running a slightly out of date version of Galaxy (I think it is change set 11080:87b586afb054) because this is BioTeam’s Slipstream appliance. Is there any chance this is a known bug? I didn’t see anything in Trello, but I’m really not sure I’ve got the hang of Trello yet. Thanks -john
The API interface is translating my parameters into python repr strings instead of actual strings. A command that should look like this: createPrimerFile.py /minilims/galaxy-data/primerTemplates/nextera.2x.primers.fasta NNNNNN NNNNNN > /slipstream/galaxy/production/data/files/020/dataset_20664.dat is getting run as this: createPrimerFile.py /minilims/galaxy-data/primerTemplates/nextera.2x.primers.fasta __lt__galaxy.tools.parameters.basic.RuntimeValue object at 0x792be10__gt__ NNNNNN > /slipstream/galaxy/production/data/files/020/dataset_20728.dat The input table in the tool info page is: Input Parameter Value Note for rerun chemistry type: <galaxy.tools.parameters.basic.RuntimeValue object at 0x7fee4425ca10> First barcode NNNNNN Second (optional) barcode NNNNNN I’m running a slightly out of date version of Galaxy (I think it is change set 11080:87b586afb054) because this is BioTeam’s Slipstream appliance. Is there any chance this is a known bug? I didn’t see anything in Trello, but I’m really not sure I’ve got the hang of Trello yet. Thanks -john
I’ve figured this one out. The tool id changed one me. Sorry for the spam. -j On Apr 9, 2014, at 4:48 PM, John Marmaduke Eppley <jmeppley@mit.edu> wrote:
The API interface is translating my parameters into python repr strings instead of actual strings.
A command that should look like this: createPrimerFile.py /minilims/galaxy-data/primerTemplates/nextera.2x.primers.fasta NNNNNN NNNNNN > /slipstream/galaxy/production/data/files/020/dataset_20664.dat
is getting run as this: createPrimerFile.py /minilims/galaxy-data/primerTemplates/nextera.2x.primers.fasta __lt__galaxy.tools.parameters.basic.RuntimeValue object at 0x792be10__gt__ NNNNNN > /slipstream/galaxy/production/data/files/020/dataset_20728.dat
The input table in the tool info page is: Input Parameter Value Note for rerun chemistry type: <galaxy.tools.parameters.basic.RuntimeValue object at 0x7fee4425ca10> First barcode NNNNNN Second (optional) barcode NNNNNN
I’m running a slightly out of date version of Galaxy (I think it is change set 11080:87b586afb054) because this is BioTeam’s Slipstream appliance. Is there any chance this is a known bug? I didn’t see anything in Trello, but I’m really not sure I’ve got the hang of Trello yet.
Thanks -john
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John Eppley -
John Marmaduke Eppley