Hi Lance,

Thank you for the pull request. I think this is an excellent way to handle patches until the toolshed itself provides a better mechanism, particularly for the devteam owned repositories; other repository owners may prefer different methods of providing patches, but they can be contacted directly by using the contact form on the toolshed. Future enhancements to the toolshed will integrate better methods of providing this functionality, but that likely some ways off. Any suggestions and community contributions on this would be appreciated. 

FreeBayes has been updated in the Toolshed to 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf, with mostly minor differences from your pull request. Please let us know if you experience any issues installing or using the updated version (0.0.3).



On Aug 30, 2012, at 11:35 AM, Lance Parsons wrote:

I have been using the FreeBayes tool in our local Galaxy instance for some time.  As FreeBayes is a rapidly evolving tool, it has been very helpful to have Daniel Blankenberg work on keeping an updated wrapper.

Recently, I've run into a rather troublesome bug in FreeBayes (https://github.com/ekg/freebayes/issues/22) that is causing it to crash on nearly every real dataset.  Luckily, the bug has been fixed in the latest version of FreeBayes (0.9.6_9608597d12e127c847ae03aa03440ab63992fedf).

Unfortunately, the latest version has a few parameter changes that require an update to the wrapper code. I've taken the liberty to make some changes to the wrapper and they seem to work. However, now that I have the tool installed from the Tool Shed, I'm not sure of the best way to 1) incorporate this update into my local galaxy instance and 2) contribute this change back to the Tool Shed.

The best solution is to get the Tool Shed updated and then pull that update into my production Galaxy instance, however, I'm wondering if there is a way I could push "hot-fixes" to my production instance without causing me headaches down the line when the Tool Shed is inevitably updated.

As far as coordinating updates of Tool Shed tools, I suppose the process might be different for different tool authors. I was wondering, however, if anyone had thoughts on how this might work best. I've created a clone of the galaxy tool shed repository in Bitbucket (https://bitbucket.org/lance_parsons/freebayes/) and given Daniel and Greg access to it in hopes that would make things easier. Let me know if there is a better way to coordinate, etc.

Thanks again.

Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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