Hi Lance,

Thank you for finding this issue and a bigger thanks for the patch. We've 
updated FreeBayes in the toolshed with your patch. Please let us know if you 
encounter further issues.



On Sep 11, 2012, at 5:08 PM, Lance Parsons wrote:

> Today I ran into a new issues with installing a specific version of 
> Freebayes.  It turns out to be an issue with how git deals with submodules, 
> something I'm only just learning about myself.  In order to ensure that 
> FreeBayes is built with the correct versions of all of the various submodules 
> for the desired revision, it seems that two commands are needed:
> git checkout 9608597d12e127c847ae03aa03440ab63992fedf
> git submodule update --recursive
> In the current version of tool_dependencies.xml, there is a git reset --hard 
> 9608597d12e127c847ae03aa03440ab63992fedf which seems to work similarly to the 
> checkout command above, however, it does not put the submodules back at the 
> correct revisions.  That is only now an issue since they were updated only 
> recently.
> I've attached a patch to the tool_dependencies.xml file that should once 
> again allow FreeBayes to be built and installed automatically.  It would be 
> great if you could update the Tool Shed repo.  Thanks.
> -- 
> Lance Parsons - Scientific Programmer
> 134 Carl C. Icahn Laboratory
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
> <freebayes_build.patch>

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