What's going on here is probably that the snpEff output is being sanitized by
galaxy prior to display. The data is all intact, and I've recently added a
config option 'sanitize_all_html' in changeset 6788:e58a87c91bc4 that will
allow you to disable this for your local instance. If you update your local
instance and set sanitize_all_html = False in your universe_wsgi.ini, you
should see the expected output.
On Feb 22, 2012, at 3:36 PM, Jennifer Jackson wrote:
> Hello Raj,
> This tool is from the Tool Shed and is maintained by the tool author. To
> contact them about functionality or problems, go to the Tool Shed at
> http://toolshed.g2.bx.psu.edu/, locate the repository (search by 'snpEff'),
> click on the name, in the the top far right corner locate the pull down menu
> "Repository Actions". Select "Contact repository owner" to send them a
> There have been many updates to Galaxy recently and it is possible that one
> of these had an impact on this tool. I am going to send your email to
> galaxy-...@bx.psu.edu, to see if anyone else has had problems with this tool
> since the last distribution update.
> You may be asked to provide more information (be as specific as you can): the
> hg pull #, any customizations, python version, etc.
> Galaxy team
> On 2/14/12 8:28 PM, Praveen Raj Somarajan wrote:
>> Hi All,
>> I updated galaxy recently to the latest version. Everything looks fine,
>> except snpEff report html view. It was displaying properly (all tables
>> and summary values) before the update, but the summary values are not
>> displaying after the update. A sample screen-shot is attached for your
>> reference. Could you please figure out this issue?
>> When I ran the same on command line, the reports were generated
>> correctly. I assume, something (datatypes or preview) has changed by the
>> update. Please let me know the work around on this?
>> Secondly, as we know, snpEff also generates a gene-wise annotation file
>> along with other results, but somehow we cannot access this file through
>> Galaxy. Though we see the link in the html report, but it seems the path
>> is broken.
>> Let me know your suggestions.
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> Jennifer Jackson
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org. Please keep all replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at: