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.belgin@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!
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___________________________________________________________
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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