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.


On Wed, May 16, 2012 at 1:08 PM, David Hoover <>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
> >
> > ___________________________________________________________
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