unsubsacrb On Thu, Feb 23, 2012 at 12:00 PM, <galaxy-dev-request@lists.bx.psu.edu>wrote:

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Today's Topics:

1. Re: Error 500 when trying to execute a workflow with the API (Anthonius deBoer) 2. Re: Error 500 when trying to execute a workflow with the API (dannonbaker@me.com) 3. Re: Splitting large jobs over multiple nodes/CPUs? (Peter Cock) 4. Re: Splitting large jobs over multiple nodes/CPUs? (dannonbaker@me.com) 5. FastX tools (Borrone, James) 6. snpEff: html report is not displaying after update (Jennifer Jackson) 7. R scripts for DESeq (Jennifer Jackson) 8. limited tool shed browse (David Hoover) 9. Re: FastX tools (Peter Cock) 10. Re: limited tool shed browse (Greg Von Kuster) 11. Re: R scripts for DESeq (Vipin TS) 12. Re: limited tool shed browse (David Hoover) 13. Re: limited tool shed browse (Greg Von Kuster) 14. Re: How to learn about new tools in the official Tool Shed (Jennifer Jackson) 15. Re: R scripts for DESeq (Liusong Yang) 16. Re: R scripts for DESeq (Greg Von Kuster) 17. Re: uploads stuck in history (Bossers, Alex) 18. Re: R scripts for DESeq (Christian Cole) 19. Re: R scripts for DESeq (Vipin TS) 20. Re: Splitting large jobs over multiple nodes/CPUs? (Peter Cock)

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Message: 1 Date: Wed, 22 Feb 2012 18:09:40 +0000 (GMT) From: Anthonius deBoer <thondeboer@me.com> To: Dannon Baker <dannonbaker@me.com> Cc: Galaxy-dev <galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] Error 500 when trying to execute a workflow with the API Message-ID: <ddf015a9-c563-e45d-cb06-af4780110d91@me.com> Content-Type: text/plain; charset="utf-8"; Format="flowed"

Huh? I have many string inputs to some particular workflow steps...Those are parameters etc that need to be entered or chosen from a dropdown..How would we deal with those kinds of entries into a workflow in the API? Or do all of them have to be pre-set?

Thanks

Thon?

On Feb 21, 2012, at 04:21 PM, Dannon Baker <dannonbaker@me.com> wrote:

...

There is no string input. If the string you're looking for is, say, the name of a dataset what you'd do is make separate calls to the history and workflow API.

For example, if you had a history "My important history", and a dataset "My input dataset", and no knowledge of the id's (as you shouldn't' have to have, externally), it'd be three separate calls. One to list histories, then you would programmatically grab the one you want ("My important history") and the ID associated with it. Then you'd make a call to grab the contents of that history, from which you could extract the id of the dataset you had the name of. And from there you know how to execute a workflow with that id (hda, in this case).

-Dannon

On Feb 21, 2012, at 7:13 PM, thondeboer@me.com wrote:

...

One more question... How do I pass a string value to one of the workflow input steps? Is there an equivalent of ldda and hda, maybe "str"..

So 38=str="Some value"

Where could I find a list of the expected dataset sources?

Thanks

Thon

On Feb 21, 2012, at 03:46 PM, Dannon Baker <dannonbaker@me.com> wrote:

...

Hi Thon,

You have the right idea about what's going wrong here. Galaxy is trying to pull up a library dataset with the ID you specify, but it doesn't exist.

In this context, src refers to the 'type' of dataset input id, more specifically whether it's from a history or library. 'hda' indicates that the dataset is from a history, and 'ldda' is what you'll most likely use in the case of a library dataset. If you browse the history and library API functionality, you'll see other methods for explicitly grabbing these ids.

My hunch is that you have an id from a history and that you should swap ldda to hda and give it another shot. Definitely let me know if you run into more issues, though, and I'll help figure out what's going on.

-Dannon

On Feb 21, 2012, at 6:22 PM, thondeboer@me.com wrote:

...

Hi,

I tried to run a workflow with the API, but get an Error 500 when I try to run the WF...The paster.log shows the following error...

$ workflow_execute.py 92cc01ed93dc0f0fc91e3ded35497c0a http://srp106:8080/api/workflows ebfb8f50c6abde6d 'TEST the API' '1=ldda=7c5ebce002fc9d5c'

Paster.log galaxy.web.framework ERROR 2012-02-21 14:36:33,067 Uncaught exception in exposed API method: Traceback (most recent call last): File "/home/tdeboer/code/galaxy-central/lib/galaxy/web/framework/__init__.py", line 145, in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ), indent=4, sort_keys=True ) File "/home/tdeboer/code/galaxy-central/lib/galaxy/web/api/workflows.py", line 123, in create hda = ldda.to_history_dataset_association(history, add_to_history=add_to_history) AttributeError: 'NoneType' object has no attribute 'to_history_dataset_association' 172.16.108.6 - - [21/Feb/2012:14:36:32 -0700] "POST /api/workflows?key=92cc01ed93dc0f0fc91e3ded35497c0a HTTP/1.1" 500 - "-" "Python-urllib/2.6"

Any ideas?

Also...I had a hard time finding out what I should use for the dataset source parameter "src" in "step=src=dataset_id" and just tried ldda, but would hope there is a little info on what this hda and ldda is?

Thanks,

Thon ___________________________________________________________ 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:

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