[galaxy-dev] Problem - submit job with PBS Torque

2012-06-01 Thread Marc Bras 
Hi !!

I've got a problem with PBS when I want to submit a job to our cluster with 
Galaxy.
Every time, PBS says me pbs_submit failed, PBS error 15023: Bad user - no 
password entry.

Indeed, Galaxy uses my email address (used in Galaxy) as user by default !
But, before, when I used SGE on my previous lab, Galaxy used the galaxy owner 
user and not my email…

Is it possible to set the owner user as previous Galaxy version ? (I found the 
drmaa_external_* session in universe but I don't really understand how to 
configure this part…).

Thanks a lot,

Best Regards


BRAS Marc___
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[galaxy-dev] Submitting jobs with PBS

2012-05-29 Thread Marc Bras 
Hi !!

I've got a problem with PBS when I want to submit a job to our cluster with 
Galaxy.
Every time, PBS says me pbs_submit failed, PBS error 15023: Bad user - no 
password entry.

Indeed, Galaxy uses my email address (used in Galaxy) as user by default !
But, before, when I used SGE on my previous lab, Galaxy used the galaxy owner 
user and not my email…

Is it possible to set the owner user as previous Galaxy version ? (I found the 
drmaa_external_* session in universe but I don't really understand how to 
configure this part…).

Thanks a lot,

Best Regards


BRAS Marc

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[galaxy-dev] Problem uploading file by an URL

2011-12-20 Thread Marc Bras 

Hi,

We have a Galaxy server in production and I have a problem when I want 
to download a huge file with HTTP URL.
Galaxy starts well to download my file, but Galaxy writes this file in 
/ tmp directory.


Is it possible to change this directory ?

Thank you,

Regards,


Marc Bras

--
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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Re: [galaxy-dev] Huge Output Files in Galaxy (in compute cluster)

2011-04-29 Thread Marc Bras 

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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