[Bio-Linux] Galaxy updates on Bio-Linux

[Tim Booth]

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