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 ( http://dev.list.galaxyproject.org/environment-variables-and-paths-for-toolshed-tools-td4656231.html), 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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