Can you clarify the steps you took that produced the behavior? See my
Anton Nekrutenko wrote:
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
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).
Are you using the Galaxy upload utility to create an item in your
history that points to the dataset file on disk?
I am not sure what is the rationale
> behind that. Ideally I think there should be no need to upload
> heavy files into the workspace.
A data file that originates from a place external to Galaxy must be
uploaded into Galaxy so that the disk file can be placed in the location
configured in the Galaxy config file. Also, when data is uploaded to
Galaxy ( either to a history or a library ), several database table
settings are created that are used by various Galaxy features.
They could actually be used straight
> away by the path specified.
What do you mean by "the path specified"?
Also is there any way to access the
> scripts for analysis on the command line. I know this undermines
> main aim of working with galaxy but rite now I am concerned about the
You should be able to run any Galaxy tool from the command line as long
as you have all of the tool's required binaries in your path. However,
running a tool from within Galaxy should generally not be any slower
than running it outside of Galaxy, depending, of course, on what you are
> I will be happy to discuss more about this in case you have some
> comments/questions for me.
> 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
> galaxy-user mailing list
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