Re: [galaxy-dev] Running a workflow programatically
On Mar 16, 2011, at 5:43 PM, Darren Brown wrote: However, when I run a workflow from the command line: python /mnt/galaxy/galaxy_dist/scripts/api/workflow_execute.py api-key url/api/workflows 38247d270c7cb1bb 'hist_id=38247d270c7cb1bb' '1=hda=30fc17ce78176bfb' My hunch is that the step id '1' in this line is probably your issue. To list workflow details in the api, you can use the scripts/api/display.py So, for your workflow there, python /mnt/galaxy/galaxy_dist/scripts/api/display.py api_key http://localhost:8080/api/workflows/38247d270c7cb1bb Check that with the workflow in question and see what it returns as the inputs dictionary. -Dannon ___ 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] Running a workflow programatically
Ah ok, and you are right there is something wrong there. The inputs
dictionary is empty:
inputs: {}
However this seems kind of odd, because I do need to specify history
inputs for the workflow through the web ui.
On Wed, Mar 16, 2011 at 2:55 PM, Dannon Baker dannonba...@me.com wrote:
On Mar 16, 2011, at 5:43 PM, Darren Brown wrote:
However, when I run a workflow from the command line:
python /mnt/galaxy/galaxy_dist/scripts/api/workflow_execute.py
api-key url/api/workflows 38247d270c7cb1bb
'hist_id=38247d270c7cb1bb' '1=hda=30fc17ce78176bfb'
My hunch is that the step id '1' in this line is probably your issue. To list
workflow details in the api, you can use the scripts/api/display.py
So, for your workflow there,
python /mnt/galaxy/galaxy_dist/scripts/api/display.py api_key
http://localhost:8080/api/workflows/38247d270c7cb1bb
Check that with the workflow in question and see what it returns as the
inputs dictionary.
-Dannon
___
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] Running a workflow programatically
Darren, While this is not currently possible, I'm currently finishing up a first pass on a workflow API that will allow this sort of interaction and hope to have an early version available by the end of this week. I can update you when that has been committed. -Dannon On Feb 24, 2011, at 9:29 PM, Darren Brown wrote: Hello folks, I am using a workflow that needs to be run many times on many different inputs. I have hacked around and figured out how to pull multiple inputs from a history, but I am a little baffled on how to run a galaxy workflow programatically. I have searched around fairly exhaustively and am wondering if this is something that anyone else has come across and accomplished. And links or pointers? Take care, Darren ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Running a workflow programatically
Hello Dannon, That is surprising and excellent! Can't wait to hear more. Take care, Darren On Wed, Mar 2, 2011 at 11:38 AM, Dannon Baker dannonba...@me.com wrote: Darren, While this is not currently possible, I'm currently finishing up a first pass on a workflow API that will allow this sort of interaction and hope to have an early version available by the end of this week. I can update you when that has been committed. -Dannon On Feb 24, 2011, at 9:29 PM, Darren Brown wrote: Hello folks, I am using a workflow that needs to be run many times on many different inputs. I have hacked around and figured out how to pull multiple inputs from a history, but I am a little baffled on how to run a galaxy workflow programatically. I have searched around fairly exhaustively and am wondering if this is something that anyone else has come across and accomplished. And links or pointers? Take care, Darren ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
