Re: [galaxy-dev] Looking for recommendations: How to run galaxy workflows in batch
Hi Dev-Team, are you planning or maybe working on an update which enables the possiblilty to run workflows in batch mode with paired end data? Cheers, Sascha
Hi, In case you'd be interested: we use a script that creates interlaced data of paired end data. We run this outside galaxy on groups of samples ordered in directories at once. We then import the interlaced data into galaxy, enabling batch workflow. The first step of the workflow is a deinterlacing of the datafiles. The script is available here: http://geertvandeweyer.zymichost.com/index.php?page=read&id=27 Best Regards, Geert On 07/18/2012 02:38 PM, Sascha Kastens wrote:
Hi Dev-Team,
are you planning or maybe working on an update which enables the
possiblilty to run workflows in batch mode with paired end data?
Cheers,
Sascha
___________________________________________________________ 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:
-- 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
Hi all, After some fiddling, I've put together an api-based workflow runner. It allows you to start workflows on batches of paired-end data from the commandline, and if set in the galaxy-config, output results to a different user (making history sharing/cloning obsolete from adminuser to end-user). Needed input (which workflow, which history, which input datafiles (from history/library) are selected on runtime by fetching the the options using the api. I've also put some notes together on the following page, regarding the api-syntax: http://tinyurl.com/cv6zmz2 It's using urllib to post the sumbission to a remote galaxy-server, so you don't need access to the galaxy-installation to run ./submit.py or ./workflow_execute.py. It's a stand-alone script, with no dependencies on the galaxy-provided code. I hope this helps some people getting started with the galaxy-api :-). Best, Geert On 07/18/2012 02:38 PM, Sascha Kastens wrote:
Hi Dev-Team,
are you planning or maybe working on an update which enables the
possiblilty to run workflows in batch mode with paired end data?
Cheers,
Sascha
___________________________________________________________ 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:
-- 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
Hi Geert, I did something similar but two things I got stumped on and maybe you found a way to do this through the API. 1) I would like to put some of my results into a datalibrary. But i can't find the API call for that. Do you know if this is possible? I asked repeatedly here on the dev list but no one seems to know if this is possible... 2) I am trying to pass my workflow some parameters that are defined in the workflow with ther ${NameOfVarible} notation. It works great in the UI, but I cannot seem to figure out how to pass parameters to a workflow... Any ideas there? Bedankt! Thon On Nov 02, 2012, at 05:39 AM, Geert Vandeweyer <geert.vandeweyer2@ua.ac.be> wrote: Hi all, After some fiddling, I've put together an api-based workflow runner. It allows you to start workflows on batches of paired-end data from the commandline, and if set in the galaxy-config, output results to a different user (making history sharing/cloning obsolete from adminuser to end-user). Needed input (which workflow, which history, which input datafiles (from history/library) are selected on runtime by fetching the the options using the api. I've also put some notes together on the following page, regarding the api-syntax: http://tinyurl.com/cv6zmz2 It's using urllib to post the sumbission to a remote galaxy-server, so you don't need access to the galaxy-installation to run ./submit.py or ./workflow_execute.py. It's a stand-alone script, with no dependencies on the galaxy-provided code. I hope this helps some people getting started with the galaxy-api :-). Best, Geert On 07/18/2012 02:38 PM, Sascha Kastens wrote: Hi Dev-Team, are you planning or maybe working on an update which enables the possiblilty to run workflows in batch mode with paired end data? Cheers, Sascha ___________________________________________________________ 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: http://lists.bx.psu.edu/ -- 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 ___________________________________________________________ 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: http://lists.bx.psu.edu/
participants (3)
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Anthonius deBoer -
Geert Vandeweyer -
Sascha Kastens