This was addressed in 6788:e58a87c91bc4.  The reason for the initial change 
that's causing 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, John David Osborne wrote:

> 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
> 
> The report looks great when generated from the command line or even if the 
> files from galaxy are copied over to a local machine and displayed.  However 
> in galaxy it appears that the supplementary data file (for example 
> dataset_41.dat.genes.txt) from the original dataset_41.dat is not accessible 
> to the main html file although I can copy it off the server. Perhaps the data 
> file it is being called from elsewhere at this is a path related issue? The 
> html looks for the data file in the same directory which I think is quite 
> reasonable.
> 
> I'm not sure which galaxy update broke this, but it is definitely broken and 
> I'm guessing any efforts to display html reports in galaxy that involve other 
> supplementary data files may be broken too….
> 
>  -John
> 
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