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 message. 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-dev@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. Regards, Jen 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.

Best,

Raj

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