Abhishek: Let talk. This is the area of active current development. We are looking at implementing a universal fastq-like format or supporting multiple formats. Perhaps we should join efforts in ironing out specifications. anton galaxy team On Jul 20, 2009, at 5:18 PM, Abhishek Pratap wrote:
Hi All
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 performance/time.
I will be happy to discuss more about this in case you have some comments/questions for me.
Best, -Abhi
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Abhishek Pratap
Bioinformatics Software Engineer
Institute for Genome Sciences
School of Medicine, Univ of Maryland
801, W. Baltimore Street, Baltimore, MD 21209
Ph: (+1)-410-706-2296
www.igs.umaryland.edu/ _______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
Anton Nekrutenko http://nekrut.bx.psu.edu http://galaxyproject.org