It is set to "False", but my galaxy runs jobs locally, not on a cluster...
(at least, not directly through the SGE Runner).
Does this work with local-runner too (i.e. starting a new process to set the metadata) ?
Also, does the "external" method works when the use changes the type in the
"Edit Attributes" page ?
Greg Von Kuster wrote, On 01/08/2010 10:54 AM:
Hello Assaf,
Is your instance configured to set metadata externally ( on your cluster
nodes )? If not, in your universe_wsgi.ini file, add the following to
the [app:main] section:
set_metadata_externally = True
On Jan 6, 2010, at 5:13 PM, Assaf Gordon wrote:
> Hello all,
>
> Continuing the search for slowness in my local Galaxy server (see
>
http://lists.bx.psu.edu/pipermail/galaxy-dev/2009-December/001549.html ),
>
> The datatypes/sequence.py file is also scanning and parsing entire
> files when creating a new FASTA/FASTQ file.
> It's nice and fun and informative for small files, but with a 2.7GB
> FASTA file - the python process stays at 100% CPU for a long long
> time, causing everything else to be very slow.
>
> The offending code is at sequence.py, method "set_meta", lines 30-39.
>
> I think Illumina expects 25x coverage of the human genome in a single
> run by the end of the year - this will roughly translates to 8 FASTQ
> files of more than 8GB each => FASTA files of 4GB each... Galaxy will
> not be able to just casually scan these files.
>
> -gordon
>
>
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Greg Von Kuster
Galaxy Development Team
greg(a)bx.psu.edu