I recently came to know about NGS analysis on galaxy during ISMB.
Getting excited I tried couple of things basically to play with it.
Few comments : I may have interepretted something described below in a
wrong way. My apologies before hand.
On a standalone installation of galaxy while I was trying to explore
one FASTQ(sequence) file. It takes considerable (> 20 min) for a fastq
file to get uploaded (2 GB). I am not sure what is the rationale
behind that. Ideally I think there should be no need to upload such
heavy files into the workspace. They could actually be used straight
away by the path specified. Also is there any way to access the
scripts for analysis on the command line. I know this undermines the
main aim of working with galaxy but rite now I am concerned about the
I will be happy to discuss more about this in case you have some
comments/questions for me.
Bioinformatics Software Engineer
Institute for Genome Sciences
School of Medicine, Univ of Maryland
801, W. Baltimore Street, Baltimore, MD 21209