Hi Greg, Anton and all
Just wondering if there has been any progress made on this end. I am sorry I was not able to follow it up on Assaf's suggestion due to other things at work.
I did try the latest version of galaxy and looks like the files are still transferred over HTTP before they could be used in the galaxy workspace. Also I would again like to highlight that many labs might want to use the local instance of galaxy and prefer to point to a local path where the file is being stored. That way we will have both the benefits of using a cool GUI and process data stored locally.
Let me know if you guys need some feedback or have more questions. I will be happy to discuss them.
best,
-Abhi
On Tue, Jul 21, 2009 at 4:26 PM, Greg Von Kuster <
ghv2@psu.edu <mailto:
ghv2@psu.edu>> wrote:
Hello Abishek,
We are currently in the process of significantly enhancing the
current Galaxy upload utilities, and the new version should
eliminate the issue you've raised about the time needed to upload
large files via HTTP ( not for making an initial copy of the file in
the Galaxy environment ). However, it will probably not be ready for
release for a few more weeks, so if you can take advantage of
Assaf's script in the meantime, that's great.  I can't guarantee
that all Galaxy features will function correctly if you do this though.
Assaf, have you found that using your script breaks anything?
Also, if you upload a file to a library rather than a history,
multiple users can "import" the library dataset into their history
for analysis, but there is only 1 file on disk ( users are pointing
to it from their histories ).  But uploading a file to a history
will create a new copy of the file each time it is uploaded.
Greg Von Kuster
Galaxy Development Team
Abhishek Pratap wrote:
Hi All
@Greg : Please find my comments below.
On Tue, Jul 21, 2009 at 10:44 AM, Greg Von Kuster<
ghv2@psu.edu
<mailto:
ghv2@psu.edu>> wrote:
Hello Abhi,
Can you clarify the steps you took that produced the
comments below.
Anton Nekrutenko wrote:
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).
Are you using the Galaxy upload utility to create an item in
your history
that points to the dataset file on disk?
Yes that is precisely correct, I am trying to upload a solexa FASTQ
file but on a standalone galaxy installation from my local file
system.
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.
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
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
Thanks for the clarification but I am not sure this will help a
lot of
people who are interested to install and run galaxy locally
mainly for
the following reasons. May be it is just local to me.
A. We already one instance of data saved on the local file system
B. Making another copy via galaxy will eat away a lot of space
in long run.
C. The time needed to import the files into galaxy space is huge
away by the path specified.
What do you mean by "the path specified"?
Well what I mean was a way to specify the path of the file/run
on the
lcoal file system and galaxy could directly pick it up from there
rather than uploading it into its own space. Now I understand this
might not work based on the way the system was designed.
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.
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.
a tool from within Galaxy should generally not be any slower
than running it
outside of Galaxy, depending, of course, on what you are doing.
Ok I was under the impression that running from SHELL will eliminate
the step of uploading them into galaxy file space.
-Abhi
I will be happy to discuss more about this in case
you have some
comments/questions for me.
Best,
-Abhi
-----------------------------
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/ <http://www.igs.umaryland.edu/>
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