Bjorn, Please direct all Galaxy development questions to the -dev list (cc'd); this ensures that they get answered quickly and by the right people.

i will put it in the toolshed. I had a few additional questions in the Issue-Tracker, but unfortunately i can't access it. Is that intentional?

Yes, we've disabled Bitbucket tickets for now. We've evaluating better ways to track issues/enhancements, and, one way or another, we'll soon have a public form of issue/enhancement tracking again.

In the pull request was one commit, that includes the index-infrastructure for bismark indices. Is that also possible with the toolshed currently?

I think so, but I'll let Greg provide the definitive answer.

Bismark is a single perl script, its ok to ship that script with the wrapper and do not fetch it via tool_dependencies.xml or?

Greg is the best person to answer this question. J.