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 <n...@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

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