I still haven't heard back from the Bio-Linux guys regarding how to update
Galaxy within Bio-Linux...

In the meantime, I tried to play with the "Manage data libraries", in order
to import large datasets. I modified the "library_import_dir" line in the
universe_wsgi.ini. The first thing I can say is that when you make a
mistake in the path (e.g. "../../directory" instead of
"../../../directory"), Galaxy won't start at all! Anyway, even now that I
figured that out, "This dataset is uploading" stays forever. As a test, I
tried to upload small dataset using the usual way ("Get Data"), and here
too "Dataset is uploading" stays forever. If I revert the
"library_import_dir" to normal, I can upload via "Get Data".

Is this also an issue related to the Galaxy version I'm using? Or is the
Galaxy in Bio-Linux screwed up?

Many thanks,


2013/2/13 David Joly <idj...@gmail.com>

> This could be the problem, I just installed BioLinux 7 on my computer with
> Galaxy running out-of-the-box...
> However, it looks like they changed a few things, there is no .hg file and
> no galaxy-dist folder. Can I update outside of mercurial?
> 2013/2/13 Dannon Baker <dannon.ba...@gmail.com>
>> How old is the galaxy you're running?  To use the main toolshed you'll
>> need to use a galaxy-dist release from December or later.  After this point
>> in time the interface was standardized and is backwards compatible.
>> To update, you should be able to simply navigate to your galaxy-dist
>> directory, 'hg pull -u', and you'll be off and running.
>> Also, since this deals with a local install, please do keep replies on
>> the 'galaxy-dev' list that I transitioned this thread to instead of
>> galaxy-user.
>> Thanks!
>> -Dannon
>> On Feb 13, 2013, at 6:43 PM, David Joly <idj...@gmail.com> wrote:
>> > Ok, one more step closer (I thought closing the browser would be enough
>> to restart galaxy, but obviously, I had to reboot the computer).
>> >
>> > But now it says: ValueError: too many values to unpack
>> >
>> >
>> > 2013/2/13 Dannon Baker <dannon.ba...@gmail.com>
>> > On Feb 13, 2013, at 6:16 PM, David Joly <idj...@gmail.com> wrote:
>> >
>> > > Hi!
>> > >
>> > > Ok, I know many people had the same issue, but I just can't figure
>> what's going on. I'm quite new about using a local instance of Galaxy and
>> I'm trying to figure how to install a tool from the tool shed. Reading the
>> tutorial  (Installing Galaxy tool shed repository tools into a local Galaxy
>> instance) looked pretty simple, but maybe I missed something.
>> > >
>> > > First, I modified the universe_wsgi.ini file by removing the "#"
>> before the tool_config_file and tool_path lines.
>> >
>> > This one step should really be all you need to do (any other files get
>> created automatically with reasonable defaults if missing) as far as
>> configuration goes.  Did you restart your galaxy instance after editing
>> universe_wsgi.ini?
>> >
>> > -Dannon
>> >
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