I'm looking for a workflow of :
Forward reads.fastq =>
QC => map => etc
Reverse reads.fastq =>
and would like to specify pairs of files (from MiSeq) in the batch workflow interface. I'm currently looking into interlacing the files outside of galaxy before uploading. Then I can de-interlace as the first step, but this is redundant, as we get seperate files to start.
Best regards,
Geert
On 05/25/2012 02:12 PM, Dannon Baker wrote:
Batch mode is currently only allowed for a single input dataset step, so the others are intentionally disabled upon toggling the first one on. We do, however, plan to eventually expand this to allow for pairwise/etc input sets. Out of curiosity, which behavior is it that you're looking for?
-Dannon
On May 25, 2012, at 8:03 AM, Geert Vandeweyer wrote:
Is it possible to use multiple 'input dataset' steps in a single workflow in batch? If I have two, I can only select batch input on one of them. If one is open, the other toggle button does not respond.
Thanks,
Geert
On 02/14/2012 09:55 PM, Petit III, Robert A. wrote:
Thats it! Consider this resolved, and total operator error. I tried using the 'Input Dataset' step, and am no longer having issues.
Thanks for the help Dannon.
From: Petit III, Robert A. Sent: Tuesday, February 14, 2012 3:49 PM To: galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] Batch limit on Wokflows
Workflow is beginning directly with a tool.
An example test workflow I've been trying is, I have 20 fasta files, and the workflow has only the FASTA-to-Tabular tool.
Thanks, Robert ________________________________________ From: Dannon Baker [dannonbaker@me.com] Sent: Tuesday, February 14, 2012 3:33 PM To: Petit III, Robert A. Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Batch limit on Wokflows
I hadn't had a chance to follow up again yet, but in your workflow, are you using an Input Dataset step, or do you have the workflow beginning directly with a tool?
-Dannon
On Feb 14, 2012, at 3:26 PM, Petit III, Robert A. wrote:
Here's the latest. I have tested this on Chrome, Firefox, and IE.
I've tried the latest revisions of galaxy-central (71031bf3105c) and galaxy-dist (26920e20157f) straight out of the box (hg clone, sh run.sh, go to localhost:8080). I am still running into same issue. All is well with 19 or less datasets in the history, but as soon as I add a 20th I can no longer run a workflow on multiple datasets.
Are there any known issues running galaxy on Ubuntu 10.04?
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Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726
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