We are using bowtie 2.1.0 in via a galaxy wrapper. Since there has been no change in the bowtie command line options used by the wrapper, there are no problems. Similar for Tophat. Brad On Apr 10, 2013, at 3:05 PM, Lance Parsons <lparsons@princeton.edu> wrote:

I noticed that the latest versions for Bowtie2 and Tophat2 listed on the Tool Dependencies page (http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies) are 2.0.4 for Bowtie2 and 2.0.6 for Tophat2. Are these the latest supported versions? Does anyone know if it's advisable to go with the latest (Bowtie2 2.1.0 and Tophat 2.0.8) with Galaxy?

I'm looking forward to these tools being moved to the ToolShed so updates to the underlying tools are accompanied by Galaxy tool version updates, but until then I'm just trying to make sure my users can use the latest versions that are compatible. Thanks.

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

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