Hi all,

When a tool is installed onto Galaxy via the GUI from the ToolShed, where is 
the tool itself installed on the system?

For instance, having installed Bed Tools from the ToolShed, the tool errors out 
on a run with the following error:

Fatal error: Exit code 127 ()
/galaxy/database/job_working_directory/000/84/tool_script.sh: line 9: bedtools: 
command not found

This means that a path needs to be set somewhere in Galaxy to the tool? Where 
is the tool installed?

Having checked the location below, only the xml files are listed.
/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/7b3aaff0d78c/bedtools<http://toolshed.g2.bx.psu.edu/repos/iuc/bedtools/7b3aaff0d78c/bedtools>

Is there a configuration that is missing?

Thanks!
Miuki Yip
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