On Tue, Sep 17, 2013 at 11:14 AM, Richard Kuo <izenkuo@gmail.com> wrote:

Hello,

It looks like the default wrapper that comes with Galaxy for Tophat2 and Bowtie2 does not include options for selecting how many threads/cores to use. Is there an easy way to get this feature in the wrappers or do I simply need to add it to the wrapper code? I

Alternatively, does anyone know of tested/debugged wrappers for Tophat2/Bowtie2 that have this feature built in?

Thank you, Richard

There seems to be agreement about how to solve this in general, which would allow the Galaxy administrator to set this on a tool by tool basis, but no implementation yet although Nate was working on one - see this thread: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-July/015735.html Peter