In the documentation page 
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax it mentions that

"the reserved parameter name GALAXY_DATA_INDEX_DIR - it points to the 

However, when we use this in a tool that is installed via toolshed we get a 
different interpretation of the variable: it seems to point to something like 
this at runtime:



Pieter Lukasse
Wageningen UR, Plant Research International
Department of Bioinformatics (Bioscience)
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
T: +31-317481122;
M: +31-628189540;
skype: pieter.lukasse.wur

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