<div dir="ltr"><div><div><div>Tim,<br><br>That was so easy. It worked! <br><br></div>I will check installing tools from the toolshed and let you know if I have problems.<br><br></div>Thank you for all your support.<br><br>
</div>Tilahun<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Aug 20, 2014 at 9:34 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 Tilahun,<br>
<br>
Thanks for your persistence. I'm sure I also saw the problem as you<br>
describe, and it was due to several Javascript libraries being missed<br>
out of the package which explains why the interface could not be drawn.<br>
<br>
I've confirmed the libraries are back in the latest package, and I have<br>
also tested it in both Chrome and Firefox and it now works for me. Are<br>
you sure that it is not a caching issue in Firefox? If you hold down<br>
"shift" and reload the page that should force a full reload. Does that<br>
help at all?<br>
<br>
Cheers,<br>
<br>
TIM<br>
<div class="HOEnZb"><div class="h5"><br>
On Wed, 2014-08-20 at 15:20 +0100, Tilahun Abebe wrote:<br>
> Tim,<br>
><br>
><br>
> I was trying different web browsers other than the default Firefox to<br>
> see if the problem I mentioned is browser-related. I opened Galaxy<br>
> from Google Chrome and it is working. I can see the Galaxy menu bar<br>
> with analyze data, shared data, administrator, users, etc. It looks<br>
> like a small tweaking is needed to open Galaxy on Firefox.<br>
><br>
><br>
> Cheers.<br>
><br>
><br>
> Tilahun<br>
><br>
><br>
><br>
> On Wed, Aug 20, 2014 at 8:52 AM, Tilahun Abebe <<a href="mailto:tilahun.abebe@uni.edu">tilahun.abebe@uni.edu</a>><br>
> wrote:<br>
> Hi Tim,<br>
><br>
><br>
> Bio-Linux is updated but there is still no change in the<br>
> appearance of Galaxy. The Galaxy menu (analyze data, shared<br>
> data, administrator, users) is not visible. I don't even see<br>
> the Galaxy logo that is normally visible on the left corner of<br>
> the menu bar. The menu bar is all black.<br>
><br>
><br>
> Thanks.<br>
><br>
><br>
> Tilahun<br>
><br>
><br>
><br>
> On Tue, Aug 19, 2014 at 11:54 AM, Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>><br>
> wrote:<br>
> Hi,<br>
><br>
> It turns out that the package didn't build properly on<br>
> Launchpad.net,<br>
> which hosts the package repository. Normally this<br>
> would have triggered<br>
> an error but in this case it just made a broken<br>
> package and I didn't<br>
> notice as my local build had worked and I had the<br>
> working files still in<br>
> the browser cache.<br>
><br>
> In any case I believe the issue is rectified. Please<br>
> install all<br>
> updates and try again.<br>
><br>
> Cheers,<br>
><br>
> TIM<br>
><br>
> On Tue, 2014-08-19 at 16:59 +0100, Tilahun Abebe<br>
> wrote:<br>
><br>
> > Tim and the Bio-Linux Community,<br>
> ><br>
> ><br>
> > Thank you for the fix to run Galaxy on Bio-Linux. I<br>
> updated Bio-Linux<br>
> > and run the command "galaxy-add-administrator". It<br>
> looks like the<br>
> > command worked this time. However, I see another<br>
> unrelated problem<br>
> > when I started Galaxy. The top Galaxy menu bar,<br>
> which lists<br>
> > administrator, users, shared files, etc is not<br>
> visible anymore. Is<br>
> > there any thing I need to do other than adding the<br>
> administrator<br>
> > e-mail address in the configuration<br>
> "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<br>
> <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>> wrote:<br>
> > Dear All,<br>
> ><br>
> > A few people have reported significant<br>
> issues with Galaxy<br>
> > Server after<br>
> > upgrading to Bio-Linux 8. Galaxy is big and<br>
> complex, has a<br>
> > large number<br>
> > of dependencies, and is being rapidly<br>
> developed, so<br>
> > maintaining it on<br>
> > Bio-Linux is always going to be a challenge.<br>
> However I have<br>
> > now updated<br>
> > the packages and made several modifications<br>
> and run through<br>
> > various<br>
> > tests, so I hope that the result, while not<br>
> perfect, will be a<br>
> > marked<br>
> > improvement.<br>
> ><br>
> > In particular, installing tools via the<br>
> "Tool Shed" should now<br>
> > work<br>
> > properly. For example, I've run through the<br>
> Galaxy 101 at<br>
> > <a href="https://usegalaxy.org/u/aun1/p/galaxy101" target="_blank">https://usegalaxy.org/u/aun1/p/galaxy101</a> and<br>
> for that you need<br>
> > to<br>
> > install the "join on genomic intervals" tool<br>
> from the tool<br>
> > shed. It<br>
> > complains it can't auto-install bx_python,<br>
> but then it works<br>
> > anyway as<br>
> > bx_python is already in the core Galaxy<br>
> package.<br>
> ><br>
> > You can also use the new reference data<br>
> management features as<br>
> > described<br>
> > here:<br>
> <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<br>
> importer and the<br>
> > BWA index<br>
> > builder by default. Others can be installed<br>
> via the Tool<br>
> > Shed.<br>
> ><br>
> > I've also put a new documentation page up at<br>
> ><br>
> <a href="http://environmentalomics.org/bio-linux-galaxy" target="_blank">http://environmentalomics.org/bio-linux-galaxy</a><br>
> explaining how<br>
> > Galaxy is<br>
> > installed on Bio-Linux and how and why this<br>
> differs from the<br>
> > "standard"<br>
> > config described on the Galaxy website.<br>
> ><br>
> > One particular thing I'm still working to<br>
> address is that<br>
> > Galaxy on<br>
> > Bio-Linux refuses to import saved histories.<br>
> 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>
> _______________________________________________<br>
> > Bio-Linux mailing list<br>
> > <a href="mailto:Bio-Linux@nebclists.nerc.ac.uk">Bio-Linux@nebclists.nerc.ac.uk</a><br>
> ><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>
> _______________________________________________<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>
><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>