[Bio-Linux] Galaxy updates on Bio-Linux
Tim Booth
tbooth at ceh.ac.uk
Wed Aug 20 10:34:03 EDT 2014
Hi Tilahun,
Thanks for your persistence. I'm sure I also saw the problem as you
describe, and it was due to several Javascript libraries being missed
out of the package which explains why the interface could not be drawn.
I've confirmed the libraries are back in the latest package, and I have
also tested it in both Chrome and Firefox and it now works for me. Are
you sure that it is not a caching issue in Firefox? If you hold down
"shift" and reload the page that should force a full reload. Does that
help at all?
Cheers,
TIM
On Wed, 2014-08-20 at 15:20 +0100, Tilahun Abebe wrote:
> Tim,
>
>
> I was trying different web browsers other than the default Firefox to
> see if the problem I mentioned is browser-related. I opened Galaxy
> from Google Chrome and it is working. I can see the Galaxy menu bar
> with analyze data, shared data, administrator, users, etc. It looks
> like a small tweaking is needed to open Galaxy on Firefox.
>
>
> Cheers.
>
>
> Tilahun
>
>
>
> On Wed, Aug 20, 2014 at 8:52 AM, Tilahun Abebe <tilahun.abebe at uni.edu>
> wrote:
> 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
>
>
>
>
>
--
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
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