<div dir="ltr"><div><div><div>Tim and the Bio-Linux Community,<br><br></div>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?<br>
<br></div>Thanks.<br><br></div>Tilahun<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Aug 19, 2014 at 8:36 AM, Tim Booth <span dir="ltr"><<a href="mailto:tbooth@ceh.ac.uk" target="_blank">tbooth@ceh.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear All,<br>
<br>
A few people have reported significant issues with Galaxy Server after<br>
upgrading to Bio-Linux 8. Galaxy is big and complex, has a large number<br>
of dependencies, and is being rapidly developed, so maintaining it on<br>
Bio-Linux is always going to be a challenge. However I have now updated<br>
the packages and made several modifications and run through various<br>
tests, so I hope that the result, while not perfect, will be a marked<br>
improvement.<br>
<br>
In particular, installing tools via the "Tool Shed" should now work<br>
properly. For example, I've run through the Galaxy 101 at<br>
<a href="https://usegalaxy.org/u/aun1/p/galaxy101" target="_blank">https://usegalaxy.org/u/aun1/p/galaxy101</a> and for that you need to<br>
install the "join on genomic intervals" tool from the tool shed. It<br>
complains it can't auto-install bx_python, but then it works anyway as<br>
bx_python is already in the core Galaxy package.<br>
<br>
You can also use the new reference data management features as described<br>
here: <a href="http://www.ncbi.nlm.nih.gov/pubmed/24585771" target="_blank">http://www.ncbi.nlm.nih.gov/pubmed/24585771</a><br>
At the moment I've included the UCSC genome importer and the BWA index<br>
builder by default. Others can be installed via the Tool Shed.<br>
<br>
I've also put a new documentation page up at<br>
<a href="http://environmentalomics.org/bio-linux-galaxy" target="_blank">http://environmentalomics.org/bio-linux-galaxy</a> explaining how Galaxy is<br>
installed on Bio-Linux and how and why this differs from the "standard"<br>
config described on the Galaxy website.<br>
<br>
One particular thing I'm still working to address is that Galaxy on<br>
Bio-Linux refuses to import saved histories. I'm not sure why this is<br>
right now. Export seems to be OK.<br>
<br>
Cheers,<br>
<br>
TIM<br>
<br>
--<br>
Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>><br>
NERC Environmental Bioinformatics Centre<br>
<br>
Centre for Ecology and Hydrology<br>
Maclean Bldg, Benson Lane<br>
Crowmarsh Gifford<br>
Wallingford, England<br>
OX10 8BB<br>
<br>
<a href="http://nebc.nerc.ac.uk" target="_blank">http://nebc.nerc.ac.uk</a><br>
<a href="tel:%2B44%201491%2069%202705" value="+441491692705">+44 1491 69 2705</a><br>
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</blockquote></div><br></div>