Hello Dannon,

Thanks for resolving the issue of snpEff HTML display. It's working well with 
the new changeset. But the gene file link in the bottom 
(dataset_*.dat.genes.txt) is still in broken state, says "could not find file". 
Any update on this?

-Raj

-----Original Message-----
From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of John David Osborne
Sent: Thursday, March 08, 2012 9:34 PM
To: Dannon Baker
Cc: galaxy-dev@lists.bx.psu.edu; David K Crossman; Pablo; 
shant...@lists.bx..psu.edu
Subject: Re: [galaxy-dev] Galaxy SNPEff Display Bug (2nd Independent Report)

Very helpful, thank you!

I don't see this option in universe_wsgi.ini, but hopefully I will when we
update our galaxy.

Thanks!

 -John



On 3/8/12 9:53 AM, "Dannon Baker" <dannonba...@me.com> wrote:

>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) 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 tooŠ.
>>
>>  -John
>>
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