Marc,

What you're seeing is likely Galaxy setting metadata like line counts, etc.  
One first step would be to check your datatypes_conf.xml and look for the 
attribute max_optional_metadata_filesize.  You can set this on a per-filetype 
basis, or, if you'd like to set it for everything, you could set your data 
entry (everything inherits from data) like so:

        <datatype extension="data" type="galaxy.datatypes.data:Data" 
mimetype="application/octet-stream" max_optional_metadata_filesize="1048576" />
 
This will tell galaxy not to set optional metadata on files larger than 1MB, 
and it might resolve the issue you're seeing.

-Dannon


On Apr 22, 2011, at 10:25 AM, Marc Bras wrote:

> Hi All, 
> 
> I use Galaxy on a compute cluster and each job is launch in a node.
> When I launch a workflow and when it generates very huge files (some Go), the 
> job finish (I can see that with 'qstat' command) but Galaxy takes several 
> minutes (or some hours !!) to display a green Box in history.
> It seems running... but it's already finished in the cluster !!
> 
> I think Galaxy is checking the output file...
> 
> Is it normal ?
> 
> Is it possible to skip this check ?
> 
> 
> Thanks in advance,
> 
> Marc
> 
> 
>  
> -- 
> Marc Bras
> 
> ------------------------------------------
> 
> 
> marc.b...@versailles.inra.fr
> 
> 
> INRA-URGI:
> Unité de Recherche Génomique Info
> Centre de Recherche de Versailles-Grignon
> Route de Saint Cyr
> 78026 Versailles - FRANCE
> 
> Tel: +33 1 30 83 34 70
> 
> ------------------------------------------
> 
> ___________________________________________________________
> 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/


___________________________________________________________
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/

Reply via email to