[Bio-Linux] Galaxy updates on Bio-Linux
Tim Booth
tbooth at ceh.ac.uk
Tue Aug 19 12:14:07 EDT 2014
Hi,
Oh dear, I just tried clearing out my browser cache and I get the same
problem. I don't know what I changed that would have caused that, but
I'll try and fix it. Sorry about that.
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
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