Re: [galaxy-dev] heads-up: more galaxy slowness in sequence.py

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 > > > _______________________________________________ > galaxy-dev mailing list > galaxy-dev(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-dev Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu