[Bio-Linux] Galaxy updates on Bio-Linux

[Tilahun Abebe]

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
>>
>
>
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