If, by "current installation methods" you are not referring to Tool Shed repository installation methods for installing tool dependencies, then please read no further. For installing tool dependencies along with repositories from the Tool Shed, fabric is currently being used. However, it's been on my list for a while to eliminate fabric if possible so that I have more management of the threads and process ids during installation. If fabric / subprocess is a problem here, I can attempt to raise the prority of looking at this. Greg Von Kuster On Nov 14, 2013, at 12:38 PM, Nate Coraor <nate@bx.psu.edu> wrote:
This is a bit tricker, since there’s currently no way to specify installation actions to run on a system other than the Galaxy application server. However, if we are saying that bash should be available to tools, I’d think there is no reason to say that it’s not expected to be available to tool installation. Unfortunately, I believe the current installation methods use subprocesses’ default, which is sh, which is not going to be bash on some systems (on Debian, it’s dash).
—nate