[Bio-Linux] Galaxy updates on Bio-Linux

[Tilahun Abebe]

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
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>
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