Hi Raj,
This is currently available in -central (https://bitbucket.org/galaxy/galaxy-central), but will be available in the next dist release. You can pull directly from central, apply the changes manually, or wait for the next dist release.
Thanks for using Galaxy,
Dan
On Mar 2, 2012, at 2:20 AM, Praveen Raj Somarajan wrote:
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:dan@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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