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 > <mailto: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 >>> >>> >>> >>> >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> >>> http://lists.bx.psu.edu/ >> >> -- >> Brad Langhorst >> langho...@neb.com <mailto:langho...@neb.com> >> 978-380-7564 >> >> >> >> > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ -- 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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