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 [dannonba...@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.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/pub/geert-vandeweyer/26/457/726
___________________________________________________________
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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--
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.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/pub/geert-vandeweyer/26/457/726
___________________________________________________________
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and other Galaxy lists, please use the interface at:
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