Dannon,
First of all, thank you for your reply !
In the datatypes_conf.xml, I attribute 'max_optional_metadata_filsize'
but it's still very long... (althought I feel it getting better).
However, when I run 'top' on the cluster computer's terminal, I see a
python script running on the master node (launching by Galaxy).
This script sets metadata.
Is it possible to launch this script on a node (and not on the master
node) ?
Thanks in advance,
Marc.
On 22/04/2011 16:39, Dannon Baker wrote:
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
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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
------------------------------------------
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