I've been doing some testing with a Galaxy instance running on my laptop for some tools we are developing. I am uploading a file into Galaxy from a URL to use as test input (~1.5GB tabular) I can download this file to my laptop in ~30 seconds with wget, while if I pull from the same URL into Galaxy it takes about 30 minutes. I set the file type so Galaxy did not have to auto-detect.
This seems very slow considering it only takes about 30 seconds to get the file over the network and write it to disk. What is Galaxy doing that makes this file upload so slow? We also tried defining our own datatype (data, not tabular with the thought that maybe Galaxy tried to examine tabular files), but it is still very slow. In production our input files will grow to be much larger than this (although we'll probably abandon tabular for a more compact binary format by then).
-- Glen L. Beane Software Engineer The Jackson Laboratory Phone (207) 288-6153