Re: [galaxy-dev] renaming fastq to fastqsanger

2012-10-17 Thread Andreas Kuntzagk 

Hi,

I have a similar problem with renaming fastq to fastqsanger. In my case after 
some time galaxy displays

An error occurred setting the metadata for this dataset. You may be able to set it manually or 
retry auto-detection.


The paster.log shows this:

galaxy.jobs DEBUG 2012-10-17 14:16:44,623 (123) Changing ownership of working directory with: 
/usr/bin/sudo -E scripts/external_chown_script.py 
/data/galaxy/galaxy-dist/database/job_working_directory/000/123 galaxy 3400
galaxy.jobs DEBUG 2012-10-17 14:16:44,989 Tool did not define exit code or stdio handling; checking 
stderr for success
141.80.188.178 - - [17/Oct/2012:14:16:45 +0200] POST /galaxy/root/history_item_updates HTTP/1.1 
200 - http://bbc.mdc-berlin.de/galaxy/history?dataset_id=f30a35c999095ed7filename=None; 
Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:16.0) Gecko/20100101 Firefox/16.0
galaxy.datatypes.metadata DEBUG 2012-10-17 14:16:45,234 setting metadata externally failed for 
HistoryDatasetAssociation 110: External set_meta() not called

galaxy.jobs DEBUG 2012-10-17 14:16:45,375 job 123 ended


May that be related to an incorrect setup of drmaa job-runner?

regards, Andreas

On 03.10.2012 18:49, Pete Schmitt wrote:


When attempting the change the filetype of a fastq file to fastqsanger, the 
process for changing the
type goes on forever. This
does not allow any further processing of the data.


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--
Andreas Kuntzagk

SystemAdministrator

Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Robert-Roessle-Str. 10, 13125 Berlin, Germany

http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich
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Re: [galaxy-dev] renaming fastq to fastqsanger

2012-10-05 Thread Peter Cock 
On Wednesday, October 3, 2012, Pete Schmitt wrote:


 When attempting the change the filetype of a fastq file to fastqsanger,
 the process for changing the type goes on forever.  This
 does not allow any further processing of the data.


That's strange - this should be really fast as it doesn't change the file
on disk, just the metadata in Galaxy's database.

(The FASTQ groomer is much slower because it does write a new file)

Which Galaxy installation was this on? If yours, do you know anything about
the setup (e.g. database used)?

Peter
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Re: [galaxy-dev] renaming fastq to fastqsanger

2012-10-05 Thread Pete Schmitt 
The installation is mine.  It's using MySQL for the db.  I have two 
other installations.  This is the only one that holds the galaxy 
database directory on an nfs mount.  The other two installations don't 
exhibit this problem.  All 3 installations run on centos 5.8 using 
python 2.6.


Sent from my iPad

On Oct 5, 2012, at 3:24, Peter Cock p.j.a.c...@googlemail.com 
mailto:p.j.a.c...@googlemail.com wrote:




On Wednesday, October 3, 2012, Pete Schmitt wrote:


When attempting the change the filetype of a fastq file to
fastqsanger, the process for changing the type goes on forever.  This
does not allow any further processing of the data.


That's strange - this should be really fast as it doesn't change the 
file on disk, just the metadata in Galaxy's database.


(The FASTQ groomer is much slower because it does write a new file)

Which Galaxy installation was this on? If yours, do you know anything 
about the setup (e.g. database used)?


Peter
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