Re: [galaxy-user] Batch jobs...

2012-10-30 Thread Dannon Baker 
They were introduced and described in this news brief (with screenshots!): 
http://wiki.g2.bx.psu.edu/DevNewsBriefs/2011_05_20

Hope this helps,

Dannon


On Oct 30, 2012, at 7:33 PM, neil.burd...@csiro.au wrote:

 Thanks Bjorn,
 But I can't seem to locate the symbol/icon (looks like papers). 
 Is there any documentation where it is located on the screen?
 
 Thanks
 Neil
 
 -Original Message-
 From: Björn Grüning [mailto:bjoern.gruen...@pharmazie.uni-freiburg.de] 
 Sent: Friday, 26 October 2012 9:47 PM
 To: Burdett, Neil (ICT Centre, Herston - RBWH)
 Cc: galaxy-user@lists.bx.psu.edu
 Subject: Re: [galaxy-user] Batch jobs...
 
 Hi Neil,
 
 if you run your workflow, there is small little symbol/icon (looks like 
 papers). If you click these ... you can select multiple input files at once. 
 Also you can probably use the Galaxy API for your task [1].
 
 Happy research!
 Bjoern
 
 [1] http://wiki.g2.bx.psu.edu/Learn/API
 
 Hi,
   I've created a workflow that works well. The workflow accepts 2 input 
 files. After uploading all my input files (there is a lot). How can I batch 
 the process, because I don't want to select files manually and run each job 
 manually. Is there a way to batch this action?
 
 Thanks
 Neil
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 --
 Björn Grüning
 Albert-Ludwigs-Universität Freiburg
 Institute of Pharmaceutical Sciences
 Pharmaceutical Bioinformatics
 Hermann-Herder-Strasse 9
 D-79104 Freiburg i. Br.
 
 Tel.:  +49 761 203-4872
 Fax.:  +49 761 203-97769
 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
 Web: http://www.pharmaceutical-bioinformatics.org/
 
 Tel.:  +49 761 203-4872
 Fax.:  +49 761 203-97769
 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
 Web: http://www.pharmaceutical-bioinformatics.org/
 
 
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Re: [galaxy-user] Batch jobs...

2012-10-30 Thread Dannon Baker 
Ahh, I see what's going on.  Galaxy relies on the Input Dataset step for this 
feature.  If you use these in your workflow, Galaxy will be able to perform the 
batch execution.  Find them in the workflow editor under Workflow control - 
inputs.

-Dannon


On Oct 30, 2012, at 8:46 PM, neil.burd...@csiro.au wrote:

 Do i need to modify a setting in universe_wsgi.ini or somewhere then ? As I 
 attach screenshots of what I've got (I have a recent subversion checkout)...
  
 Thanks
 Neil
  
  
 image001.jpg
  
  
  
 image002.jpg

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Re: [galaxy-user] Batch jobs...

2012-10-30 Thread Dannon Baker 
Connect the Input Dataset workflow step to the dataset input of the step you'd like to run multiple inputs across, like below. With that example workflow, I can select a batch of inputs that will *all* be mapped with BWA.On Oct 30, 2012, at 9:04 PM, neil.burd...@csiro.au wrote:Thanks Dannon, I can see them now but how do I use them now? As I now have 3 steps:Input File (as before)Input Dataset (new)Atlas list (as before)I select the "Input file" in step 1, and atlases in step 3 (as before) and I can select multiple files for the Input Dataset (but how does that tie into step 1 and 3 as its not connected on the workflow diagram? Neil-Original Message-From: Dannon Baker [mailto:dannonbaker@me.com] Sent: Wednesday, 31 October 2012 10:54 AMTo: Burdett, Neil (ICT Centre, Herston - RBWH)Cc: bjoern.gruen...@pharmazie.uni-freiburg.de; galaxy-user@lists.bx.psu.eduSubject: Re: [galaxy-user] Batch jobs...Ahh, I see what's going on. Galaxy relies on the "Input Dataset" step for this feature. If you use these in your workflow, Galaxy will be able to perform the batch execution. Find them in the workflow editor under "Workflow control" - inputs.-DannonOn Oct 30, 2012, at 8:46 PM, neil.burd...@csiro.au wrote:Do i need to modify a setting in universe_wsgi.ini or somewhere then ? As I attach screenshots of what I've got (I have a recent subversion checkout)...ThanksNeilimage001.jpgimage002.jpg___
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