Thanks for breaking that down for me. We are trying to set up some dev machines in our environment in a few weeks and I may create a clone of our production Galaxy mirror and play around with that version to see if I can get the functionality that I'm looking for. I'll take that idea about having a daemon into consideration.
Regards, Josh On Wed, May 16, 2012 at 1:08 PM, David Hoover <hoove...@helix.nih.gov>wrote: > No, this was all an idea I've had for a while, but never did anything > about it. I'm pretty sure the Galaxy developers are not interested in > anything this locally-centric, and I don't blame them. It ought to be > something outside the Galaxy build completely, because Galaxy is meant to > be system-independent. > > What I meant by 'joint user/galaxy directory' is a directory that is owned > by a user, but that the galaxy user has read (and possibly write) access > to. This is entirely possible given either a well-informed user > population, or an iron-clad suexec executable. > > The mechanism I alluded to is a feature by which a user can upload a > directory of files all at once. There is a configuration directive in > universe_wsgi.ini, user_library_import_dir, that allows non-administrative > users to upload an entire directory of files into a library. The directive > identifies the base directory, within which subdirectories named as the > galaxy user login (email address) are searched. The > user_library_import_dir directory is owned by the galaxy user, and the > subdirectories are owned by the user, but group owned by the galaxy user. > A user will copy files to the subdirectory, login to galaxy, switch to > their library, and upload all the files in the directory into a single > library folder. > > There isn't much documentation about it in the main Galaxy wiki, so forget > that. I haven't enabled it in our local production site, and I haven't > played with it in a long time. I'm pretty sure that the files are not > removed after uploading, and a user is free to re-upload the files again > and again, so it's kind of quirky. Also, if the files are not readable by > the galaxy user, a bizarre and unhelpful error is thrown. > > If this functionality could be extended and elaborated, it could do what > you want. The user_library_import_dir requires that the user's login in > Galaxy must be identical to the the user's login on the cluster, and that > the permissions be kept correct. Typically users have no idea what is > going on with their permissions, so what are you going to do? > > David > > On May 16, 2012, at 1:33 PM, Josh Nielsen wrote: > > > Hi David, > > > > Actually that is an interesting idea to use a daemon to move the files > into associated user directories. Is that something that Galaxy Dev is > working/can work on, or was that just a suggestion? I'm not opposed to > doing any dev work of my own, but I don't really know Python that well and > I know most of the Galaxy code is Python. > > > > I'm not sure that I follow what you are talking about with the joint > user/galaxy directory though. I'm of course wanting it to not be unified > (not all in the same directory) and rather be segregated by user into user > subdirectories, but I think you already caught that so I guess I just > didn't understand what you were getting at. > > > > Josh Nielsen > > > > ---------- > > >How about if there were a completely separate daemon that monitored the > galaxy database periodically to determine what datasets belong to which > user(s). Then > > >it would move the actual dataset to an area owned by the user and group > accessible to galaxy, replacing the dataset with a symlink. This would > require no changes to the galaxy build, but it would require a constant > monitoring system. > > > > >There is already a mechanism for users to move their files into a joint > user/galaxy directory, but it is (as far as I know) only allowed for > libraries, not > > >histories. It would be better if there were a way for users to browse > through their own directories as a tool, and be able to load files directly > into their history. > > > > > > >David Hoover > > > > ___________________________________________________________ > > 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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