Hi, Galaxy-Developers,

I apologize if this question has been answered before; I'm trying to
override a couple of environment variables on a per-tool level, for a tool
that is not installed in the toolshed.  I've read a post on the mailing
list that suggests this is possible for tools installed from the toolshed (
however I am interested in doing this for a tool not installed from the
toolshed, for example, the draw histogram tool.

Basically, it appears at this point in time that I have to have multiple
versions of R compiled to support our Galaxy instance.  This stems from
fragmented version support of different software components (for example
the new version of the Bioconductor suite (used for CummeRbund) requires R
3.x, but the draw histogram function requires rpy, which isn't supported
with R 3.x).  For what it is worth, I did read about somebody who released
a version of the draw histogram function that supports rpy2 (
http://dev.list.galaxyproject.org/rpy2-Core-Tools-td4659832.html), however
I am asking this question regardless as I do not want to go through the
exercise of testing the rpy2 core tools right now if it is not necessary.

So, my question is this; is there a preferred way to handle per-tool
overrides for environment variables such as $PATH or $RPATH, for tools
*not* included in the tool shed, for example the draw histogram tool?  It
does not appear that these tools have a tool_dependencies.xml.  I
appreciate you taking the time to answer my question and wish you a
wonderful day.

Thank you,

Dan Sullivan
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