Hi Alban,
Yes, we would very much interested in this tool, since our current workaround
is not a desired one (a python mini http server!).
Thank you for sharing it :)
-Mehmet
On Jun 8, 2012, at 4:36 AM, Alban Lermine wrote:
Hi,
There is also another solution if you don't want let users being able to
create libraries.
We have implemented this solution in our local production server here at
Institut Curie.
We add a tool call local upload file, that takes as entry parameters the
name of the dataset, the type of file and the path to the file you want to
upload.
At the execution, the bash script behind will remove the output dataset
created by Galaxy and replaced it by a symbolic link to the file (so you
don't duplicate files).
Just to warn you, there could be a security failure with this tool, because
if it is locally executed, it will be by the Galaxy applicative user that can
potentially have more rights on file than the current user.
To go through this failure, we execute this tool on our local cluster (with
pbs/torque) as the current user (so if the current user try to upload a file
that he doesn't owned, the tool will not be able to create the symbolic link
and the user will receive an error on the Galaxy interface).
Tell me if you're interested in such a tool, and I send you the xml file and
bash script associated.
Bests,
Alban
Le 07/06/2012 20:11, Mehmet Belgin a écrit :
Brad,
Thank you for your fast reply! Looks like library_import_dir is for admins
and there is another library option for users. I will try with that one and
see if the files appear in the GUI.
Thanks!
=
Mehmet Belgin, Ph.D. (mehmet.bel...@oit.gatech.edu)
Scientific Computing Consultant | OIT - Academic and Research Technologies
Georgia Institute of Technology
258 Fourth Street, Rich Building, Room 326
Atlanta, GA 30332-0700
Office: (404) 385-0665
On Jun 7, 2012, at 2:04 PM, Langhorst, Brad wrote:
Mehmet:
It's not important how the files get there, they could be moved via ftp,
scp, cp, smb - whatever.
Galaxy will use that directory to import from no matter how the files
arrive.
I found that confusing at first too.
Brad
On Jun 7, 2012, at 1:55 PM, Mehmet Belgin wrote:
Hi Everyone,
I am helping a research group to use Galaxy on our clusters. Unfortunately
I have no previous experience with Galaxy, but learning along the way. We
are almost there, but cannot figure out one particular issue. This is
about configuration of Galaxy, so I thought developers list is a better
place to submit than the user list.
The galaxy web interface allows for either copy/paste of text, or a URL.
Unfortunately we cannot setup a FTP server as instructed due to
restrictions on the cluster. The files we are trying to upload are large;
around 2GB in size. It does not make sense to upload these files to a
remote location (which we can provide an URL for) and download them back,
since the data and galaxy are on the same system. However, I could not
find a way to open these files locally.
I did some reading, and hoped that library_import_dir in
universe_wsgi.ini would do the trick, but it didn't. Therefore, I
will really appreciate any suggestions.
Thanks a lot in advance!
-Mehmet
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Brad Langhorst
langho...@neb.com
978-380-7564
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Alban Lermine
Unité 900 : Inserm - Mines ParisTech - Institut Curie
« Bioinformatics and Computational Systems Biology of Cancer »
11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France
Tel : +33 (0) 1 56 24 69 84
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