[Bio-Linux] Galaxy updates on Bio-Linux

[Tilahun Abebe]

Hi Tim,

Bio-Linux is updated but there is still no change in the appearance of
Galaxy. The Galaxy menu (analyze data, shared data, administrator, users)
is not visible. I don't even see the Galaxy logo that is normally visible
on the left corner of the menu bar. The menu bar is all black.

Thanks.

Tilahun


On Tue, Aug 19, 2014 at 11:54 AM, Tim Booth <tbooth at ceh.ac.uk> wrote:

> Hi,
>
> It turns out that the package didn't build properly on Launchpad.net,
> which hosts the package repository.  Normally this would have triggered
> an error but in this case it just made a broken package and I didn't
> notice as my local build had worked and I had the working files still in
> the browser cache.
>
> In any case I believe the issue is rectified.  Please install all
> updates and try again.
>
> Cheers,
>
> TIM
>
> On Tue, 2014-08-19 at 16:59 +0100, Tilahun Abebe wrote:
> > Tim and the Bio-Linux Community,
> >
> >
> > Thank you for the fix to run Galaxy on Bio-Linux. I updated Bio-Linux
> > and run the command "galaxy-add-administrator". It looks like the
> > command worked this time. However, I see another unrelated problem
> > when I started Galaxy. The top Galaxy menu bar, which lists
> > administrator, users, shared files, etc is not visible anymore. Is
> > there any thing I need to do other than adding the administrator
> > e-mail address in the configuration "universe_wsgi.ini" file?
> >
> >
> > Thanks.
> >
> >
> > Tilahun
> >
> >
> >
> > On Tue, Aug 19, 2014 at 8:36 AM, Tim Booth <tbooth at ceh.ac.uk> wrote:
> >         Dear All,
> >
> >         A few people have reported significant issues with Galaxy
> >         Server after
> >         upgrading to Bio-Linux 8.  Galaxy is big and complex, has a
> >         large number
> >         of dependencies, and is being rapidly developed, so
> >         maintaining it on
> >         Bio-Linux is always going to be a challenge.  However I have
> >         now updated
> >         the packages and made several modifications and run through
> >         various
> >         tests, so I hope that the result, while not perfect, will be a
> >         marked
> >         improvement.
> >
> >         In particular, installing tools via the "Tool Shed" should now
> >         work
> >         properly.  For example, I've run through the Galaxy 101 at
> >         https://usegalaxy.org/u/aun1/p/galaxy101 and for that you need
> >         to
> >         install the "join on genomic intervals" tool from the tool
> >         shed.  It
> >         complains it can't auto-install bx_python, but then it works
> >         anyway as
> >         bx_python is already in the core Galaxy package.
> >
> >         You can also use the new reference data management features as
> >         described
> >         here: http://www.ncbi.nlm.nih.gov/pubmed/24585771
> >         At the moment I've included the UCSC genome importer and the
> >         BWA index
> >         builder by default.  Others can be installed via the Tool
> >         Shed.
> >
> >         I've also put a new documentation page up at
> >         http://environmentalomics.org/bio-linux-galaxy explaining how
> >         Galaxy is
> >         installed on Bio-Linux and how and why this differs from the
> >         "standard"
> >         config described on the Galaxy website.
> >
> >         One particular thing I'm still working to address is that
> >         Galaxy on
> >         Bio-Linux refuses to import saved histories.  I'm not sure why
> >         this is
> >         right now.  Export seems to be OK.
> >
> >         Cheers,
> >
> >         TIM
> >
> >         --
> >         Tim Booth <tbooth at ceh.ac.uk>
> >         NERC Environmental Bioinformatics Centre
> >
> >         Centre for Ecology and Hydrology
> >         Maclean Bldg, Benson Lane
> >         Crowmarsh Gifford
> >         Wallingford, England
> >         OX10 8BB
> >
> >         http://nebc.nerc.ac.uk
> >         +44 1491 69 2705
> >         _______________________________________________
> >         Bio-Linux mailing list
> >         Bio-Linux at nebclists.nerc.ac.uk
> >         http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> >
> >
>
> --
> Tim Booth <tbooth at ceh.ac.uk>
> NERC Environmental Bioinformatics Centre
>
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
>
> http://nebc.nerc.ac.uk
> +44 1491 69 2705
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
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