Re: [galaxy-dev] Galaxy SNPEff Display Bug (2nd Independent Report)

2012-03-08 Thread John David Osborne
using these display issues was to eliminate potential XSS >vulnerabilities. There's now a configuration option (sanitize_all_html, >which is True by default) for local instances where you can disable the >extra html sanitization. > >-Dannon > >On Mar 8, 2012, at 10:33 AM, J

[galaxy-dev] Galaxy SNPEff Display Bug (2nd Independent Report)

2012-03-08 Thread John David Osborne
Hi Pablo, About 3 weeks ago Praveen mentioned a bug in SNPEff such that it no longer correctly displays the HTML report in galaxy – we have the exact same error. Is there a workaround for this yet? I found his original report here: http://article.gmane.org/gmane.science.biology.galaxy.user/2418

[galaxy-dev] Out of Memory Error (Galaxy Local Instance) - File Download

2011-06-01 Thread John David Osborne
Hi, We have run into a an error when trying to download a previously uploaded file from our local galaxy instance (lives in a 512 MB VM). The error is at the end of this message. In a previous thread, Nate advised setting use_debug = False in universe_wsgi.ini. Is this because the debugging cod

[galaxy-dev] Migration Bug and Fix; Additional Questions

2011-02-04 Thread John David Osborne
I ran into the error shown at the end of this email today. It looks like someone is trying to rename a sequence generator but using the wrong syntax for postogres (at least for my 8.1.2 version). Anyways, I worked around the problem by switching lib/galaxy/model/migrate/versions/0068_rename_seq

Re: [galaxy-dev] Version Error and Python 2.7

2011-02-02 Thread John David Osborne
Thanks Peter! I found 2.6 ( http://www.python.org/download/releases/2.6.6/) so I will go ahead and try that with galaxy and see if the problem goes away. -John On 2/2/11 12:07 PM, "Peter Cock" wrote: On Wed, Feb 2, 2011 at 6:02 PM, John David Osborne wrote: > I have (or

[galaxy-dev] Version Error and Python 2.7

2011-02-02 Thread John David Osborne
I have (or rather had) a functional galaxy installation on a CentOS box running python 2.4. I did an mecurial update for the first time and broke my installation. It looks like some eggs are getting out of date and when I run scramble.py I get an error (see below). I'm guessing this is because s