Hello Dan,

But, I am currently using the latest update of Galaxy (as 'hg incoming' says 
'no changes'). Just to clarify one thing: which repository should I clone - 
https://bitbucket.org/galaxy/galaxy-dist/ (mentioned in GetGalaxy.org) OR 
http://www.bx.psu.edu/hg/galaxy/ (mentioned in NewsBrief website). I use the 
first one to update Galaxy. I tried to pull the below changeset, but it says 
'invalid revision'.


Please suggest.

Best,

Raj


From: Daniel Blankenberg [mailto:d...@bx.psu.edu]
Sent: Thursday, March 01, 2012 8:45 PM
To: Praveen Raj Somarajan
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Error in DepthOfCoverage (GATK) tool

Hi Raj,

Thanks for reporting, this issue has been resolved in changeset 
6778:35be930b21be.  Please let us know if you encounter further issues.


Thanks for using Galaxy,

Dan


On Mar 1, 2012, at 3:30 AM, Praveen Raj Somarajan wrote:


Hello,

I'm facing an issue with "Depth Of Coverage" tool when it runs on refGene and 
target BED file. The error message is:

File "cheetah_DynamicallyCompiledCheetahTemplate_1330588825_26_16118.py", line 
402, in respond
NotFound: cannot find 'omit_interval_statistics' while searching for 
'gatk_param_type.omit_interval_statistics'

I noticed that the issue is only when the "Advanced GATK options" is enabled to 
set target BED file.

The commandline runs perfectly with the input files, but galaxy fails due to 
this error. Can anyone suggest what's the issue?

Best,

Raj

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