[galaxy-dev] Workflow API (runtime modification of tool parameters)

2011-12-05 Thread Richard Park
the API to allow for runtime parameter configuration? If this is the case, any pointers on how to extend this would be greatly appreciated. Thank you, Richard Park ___ Please keep all replies on the list by using reply all in your mail client

Re: [galaxy-dev] Workflow API (runtime modification of tool parameters)

2011-12-07 Thread Richard Park
with this at all.  Once it's done, if you're willing, we'd certainly like to merge the changes back in and include the functionality in the base galaxy distribution. -Dannon On Dec 5, 2011, at 5:10 PM, Richard Park wrote: Hello, I was wondering what would be the best way to extend Galaxy's

Re: [galaxy-dev] Workflow API (runtime modification of tool parameters)

2012-04-04 Thread Richard Park
. Let me know if you need any help with this at all. Once it's done, if you're willing, we'd certainly like to merge the changes back in and include the functionality in the base galaxy distribution. -Dannon On Dec 5, 2011, at 5:10 PM, Richard Park wrote: Hello, I was wondering what would

Re: [galaxy-dev] Workflow API (runtime modification of tool parameters)

2012-06-21 Thread Richard Park
into? As an aside, I'd love to look at the runtime parameter specification changes you've made for potential inclusion.  This is a feature I've wanted to add for some time. Thanks! Dannon On Apr 4, 2012, at 4:17 PM, Richard Park wrote: Hi Dannon, Thank for the pointers from before, I have

[galaxy-dev] Can't edit galaxy workflow

2012-11-09 Thread Richard Park
Hi Guys, I updated to the latest galaxy distribution today and I cant seem to edit existing workflows. I've seen others with this error from a Sept 07 distribution ( http://dev.list.galaxyproject.org/Can-t-edit-Galaxy-Workflow-ElementInterface-instance-has-no-attribute-render-td4656393.html), but

[galaxy-dev] copying files via galaxy API

2012-12-19 Thread Richard Park
Hi Everyone, Is there a way to directly copy files from galaxy with the proper file name? I'm currently using the galaxy API to download files via HTTP, but it is very slow and would like to speed up the process of copying files directly, but am having a hard time getting the proper file names.

[galaxy-dev] patch for workflow api

2013-01-30 Thread Richard Park
Hi Guys, I've just updated to the latest galaxy-central and notice a problem when trying to export workflows via the api. In galaxy-central/lib/webapps/galaxy/api/workflows.py, I just need to add in an extra tab in lines 88 and 89, the patch is below. PATCH using hg diff diff -r

Re: [galaxy-dev] patch for workflow api

2013-01-30 Thread Richard Park
:54 PM, Richard Park rp...@bu.edu wrote: Hi Guys, I've just updated to the latest galaxy-central and notice a problem when trying to export workflows via the api. In galaxy-central/lib/webapps/galaxy/api/workflows.py, I just need to add in an extra tab in lines 88 and 89, the patch is below

[galaxy-dev] How to count the number of Workflow steps?

2013-03-05 Thread Richard Park
Hi everyone, Does anybody know how Galaxy currently determines which outputs from a tool are shown when a workflow is run? I'm currently dynamically creating workflows based on the number of given inputs and iterating through all HideDatasetAction* for each tools post_job_actions to figure out the

[galaxy-dev] Workflow Actions

2013-03-05 Thread Richard Park
Hi everyone, Does anybody know how Galaxy currently determines which outputs from a tool are shown when a workflow is run? I'm currently dynamically creating workflows based on the number of given inputs and iterating through all HideDatasetAction* for each tools post_job_actions to figure out the

Re: [galaxy-dev] How to count the number of Workflow steps?

2013-03-05 Thread Richard Park
HideDatasetActions added to the step automatically. -Dannon On Tue, Mar 5, 2013 at 5:32 PM, Richard Park rp...@bu.edu wrote: Hi everyone, Does anybody know how Galaxy currently determines which outputs from a tool are shown when a workflow is run? I'm currently dynamically creating

[galaxy-dev] Cancel running jobs/workflows through API

2013-03-27 Thread Richard Park
Hey guys, I know there's no current way of canceling jobs or workflows through the API, but does anyone have any idea on how to implement this in Galaxy? i.e. where in the code base to see how galaxy is currently killing jobs. My ideal solution would be to get the list of qeued jobs for a giving

Re: [galaxy-dev] Cancel running jobs/workflows through API

2013-04-03 Thread Richard Park
/ **controllers/admin.py, in the jobs method of the Admin class. Hopefully that will provide the base structure for what you want to accomplish. --Dave B. On 3/27/13 12:02:20.000, Richard Park wrote: Hey guys, I know there's no current way of canceling jobs or workflows through the API