[Bio-Linux] Galaxy updates on Bio-Linux
Tilahun Abebe
tilahun.abebe at uni.edu
Wed Aug 20 10:46:20 EDT 2014
Tim,
That was so easy. It worked!
I will check installing tools from the toolshed and let you know if I have
problems.
Thank you for all your support.
Tilahun
On Wed, Aug 20, 2014 at 9:34 AM, Tim Booth <tbooth at ceh.ac.uk> wrote:
> 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
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.bioinformatics.org/pipermail/bio-linux-list/attachments/20140820/cd2ac868/attachment.html>
More information about the Bio-linux-list
mailing list