Hi Miuki Yip,
repositories installed from Tool Shed will be physically present on a path
defined in the config/shed_tool_conf.xml file. Look for a line looking like
this: <toolbox tool_path="../shed_tools">. The tool_path specifies path to
If the repository has tool dependencies installed as a Tool Shed packages
look into your config/galaxy.ini file for a line starting with
`tool_dependency_dir`. That will point to a path where dependencies are
Please let us know if you have more questions.
Thank you for using Galaxy.
On Mon, Nov 28, 2016 at 11:39 AM Yip, Miu ki <m...@cshl.edu> wrote:
> 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.
> Is there a configuration that is missing?
> Miuki Yip
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and other Galaxy lists, please use the interface at:
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