Hi Nate, I followed your instructions, creating a datatype and providing it. However, loading the files still takes ages (>1h); I do it as an admin, going through the following menu: Admin>Manage data libraries>[my library(GAIIx)]>Add datasets>Upload directory of files. See the attached screenshot for the parameters I set (Picture2.png). Any idea what could be the reason for it? I've attached the content of the mysql job table for that job (job.sql.txt). Here is my datatype definition in the corresponding files (datatypes_conf.xml, registry.py and tabular.py). Look for the Export Class or the export keyword. Btw the export format is an Illumina default standard, which you might want to have in Galaxy as a default :-) I haven't set the metadata information yet, but could have a look at it if you find this datatype useful and would consider adding it as a default. Thanks for your help, Nico --------------------------------------------------------------- Nicolas Delhomme High Throughput Functional Genomics Center European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delhomme@embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany --------------------------------------------------------------- On 22 Nov 2010, at 16:21, Nate Coraor wrote:
Nicolas Delhomme wrote:
Hi all,
I do see the see the same, whenever loading export (one of Illumina sequencer output) files (as an admin uploading a directory of files) or when running bowtie/bwa/samtools. I'm wondering if this would have something to do with the Sniffers (i.e. that you're validating the generated files)? Actually as I'm running a local Galaxy instance and am sure that the format are correct, being directly at the source, I would not need such validations. Is there a way to turn that off?
Nico,
If you set the file type on the upload form, the datatype will not be sniffed. In addition, setting the rest of the metadata can be sped up by setting:
set_metadata_externally = True
In universe_wsgi.ini.
--nate
Best,
Nico
--------------------------------------------------------------- Nicolas Delhomme
High Throughput Functional Genomics Center
European Molecular Biology Laboratory
Tel: +49 6221 387 8310 Email: nicolas.delhomme@embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany ---------------------------------------------------------------
On 10 Nov 2010, at 21:08, David Hoover wrote:
I've set up a local instance of Galaxy, and have submitted a lastz job on some fake data. It ran for about 3 minutes and then finished, as shown in the logfiles and by system tools like top and ps. However, the web page shows the spinning wheel and yellow box for 10 minutes until the box turned green and wheel stopped spinning.
Why is there such a delay between when the job completes and when the web page shows it is finished? Is there a configuration element I'm missing?
David Hoover Helix Systems Staff http://helix.nih.gov _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
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