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