Hi Galaxy Dev, Been having trouble getting my Galaxy tools to work with the testtoolshed. Here is the tools repository: https://jeremyjliu@testtoolshed.g2.bx.psu.edu/repos/jeremyjliu/region_motif_... In particular, I've been focusing on getting the region_motif_intersect.r script to work properly when installed from the testtoolshed. intersect.r runs using files located in the same location as where the repository is installed, in the folder region_motif_db. To make sure that the tool knows where these files are, I've been trying to pass the repository install location as an argument in the r script invocation (see region_motif_intersect.xml and tool_dependencies.xml) . To set the repository install location in the environment, I've been basing off of this wiki entry: https://wiki.galaxyproject.org/ToolsWithDependenciesInSameRepository When I install the repository to my local Galaxy, it gives me the following warnings: galaxy.tools.deps DEBUG 2014-10-25 15:12:35,376 Building dependency shell command for dependency 'R_SCRIPT_PATH' galaxy.tools.deps WARNING 2014-10-25 15:12:35,377 Failed to resolve dependency on 'R_SCRIPT_PATH', ignoring Then when I run the tool from Galaxy, this is the run command: PACKAGE_BASE=/Users/jeremyliu1/galaxy-dist/tool-dependency/R/2.15.1/jeremyjliu/region_motif_enrichment/7a3bb055f3d0; export PACKAGE_BASE; . /Users/jeremyliu1/galaxy-dist/tool-dependency/R/2.15.1/jeremyjliu/region_motif_enrichment/7a3bb055f3d0/env.sh; Rscript /Users/jeremyliu1/shed_tools/testtoolshed.g2.bx.psu.edu/repos/jeremyjliu/region_motif_enrichment/7a3bb055f3d0/region_motif_enrichment/region_motif_intersect.r --args $R_SCRIPT_PATH p /Users/jeremyliu1/galaxy-dist/database/files/000/dataset_504.dat /Users/jeremyliu1/galaxy-dist/database/files/000/dataset_515.dat What exactly is going on here? How do I make sure my tool knows where the reference files it needs are, since it won't be in the job working directory? Note: the files that intersect.r needs are not in the toolshed repository, since they are a few GB. I was planning on providing that as a separate download or using the Data Managers to solve the problem. But as long as I can get the tool to look for it in that folder, that would be perfect. Thanks! Jeremy Liu jeremy.liu@yale.edu 352.871.1258