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 >>>> >>>> >>>> >>>> >>>> >>>> ___________________________________________________________ >>>> 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 >>> 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 > ___________________________________________________________ > 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/
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