Hi Bryn,
Removing unneeded data is the best solution if using Main. One example would be saving back (locally) the original FASTQ input, then deleting it permanently from your history, rather than leaving both the raw data and the Groomed data on the server. This can actually help quite a bit if your datasets are large. See this wiki for help about Delete vs Delete Permanently: http://galaxyproject.org/wiki/Learn/Managing%20Datasets#Actions
Another option is to move to a local or cloud instance: http://getgalaxy.org
I am posting back to the mailing list along with a clearer subject line, to help others who may have a similar question.
Best,
Jen Galaxy team
On 10/25/11 10:54 AM, Bryn Gaertner wrote:
Hi Jennifer,
I am trying to run cufflinks, which I don't think should be too hard (it's on C. elegans). Do you have any suggestions for reducing the amount of memory I'm sucking?
Thanks! Bryn