Hi, 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 ~/tool-data<https://bitbucket.org/galaxy/galaxy-central/src/tip/tool-data> directory." 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: ./database/tmp/tmp-toolshed-gmfcrIr59Sq Ideas? 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 http://www.pri.wur.nl<http://www.pri.wur.nl/>