Hi Galaxy Dev,

Been having trouble getting my Galaxy tools to work with the testtoolshed.
Here is the tools repository:

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:

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:
export PACKAGE_BASE; .
--args $R_SCRIPT_PATH p

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

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.

Jeremy Liu
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