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@bx.psu.edu