<div dir="ltr"><div><div><div>Hi Tim,<br><br></div>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. <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 11:54 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">Hi,<br>
<br>
It turns out that the package didn't build properly on Launchpad.net,<br>
which hosts the package repository. Normally this would have triggered<br>
an error but in this case it just made a broken package and I didn't<br>
notice as my local build had worked and I had the working files still in<br>
the browser cache.<br>
<br>
In any case I believe the issue is rectified. Please install all<br>
updates and try again.<br>
<br>
Cheers,<br>
<div class="im HOEnZb"><br>
TIM<br>
<br>
On Tue, 2014-08-19 at 16:59 +0100, Tilahun Abebe wrote:<br>
</div><div class="HOEnZb"><div class="h5">> Tim and the Bio-Linux Community,<br>
><br>
><br>
> Thank you for the fix to run Galaxy on Bio-Linux. I updated Bio-Linux<br>
> and run the command "galaxy-add-administrator". It looks like the<br>
> command worked this time. However, I see another unrelated problem<br>
> when I started Galaxy. The top Galaxy menu bar, which lists<br>
> administrator, users, shared files, etc is not visible anymore. Is<br>
> there any thing I need to do other than adding the administrator<br>
> e-mail address in the configuration "universe_wsgi.ini" file?<br>
><br>
><br>
> Thanks.<br>
><br>
><br>
> Tilahun<br>
><br>
><br>
><br>
> On Tue, Aug 19, 2014 at 8:36 AM, Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>> wrote:<br>
> Dear All,<br>
><br>
> A few people have reported significant issues with Galaxy<br>
> Server after<br>
> upgrading to Bio-Linux 8. Galaxy is big and complex, has a<br>
> large number<br>
> of dependencies, and is being rapidly developed, so<br>
> maintaining it on<br>
> Bio-Linux is always going to be a challenge. However I have<br>
> now updated<br>
> the packages and made several modifications and run through<br>
> various<br>
> tests, so I hope that the result, while not perfect, will be a<br>
> marked<br>
> improvement.<br>
><br>
> In particular, installing tools via the "Tool Shed" should now<br>
> 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<br>
> to<br>
> install the "join on genomic intervals" tool from the tool<br>
> shed. It<br>
> complains it can't auto-install bx_python, but then it works<br>
> 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<br>
> 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<br>
> BWA index<br>
> builder by default. Others can be installed via the Tool<br>
> 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<br>
> Galaxy is<br>
> installed on Bio-Linux and how and why this differs from the<br>
> "standard"<br>
> config described on the Galaxy website.<br>
><br>
> One particular thing I'm still working to address is that<br>
> Galaxy on<br>
> Bio-Linux refuses to import saved histories. I'm not sure why<br>
> 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>
> _______________________________________________<br>
> Bio-Linux mailing list<br>
> <a href="mailto:Bio-Linux@nebclists.nerc.ac.uk">Bio-Linux@nebclists.nerc.ac.uk</a><br>
> <a href="http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux" target="_blank">http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux</a><br>
><br>
><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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</div></div></blockquote></div><br></div>