Galaxy ToolShed Installation Question

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Galaxy ToolShed Installation Question

Yip, Miu ki
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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Re: Galaxy ToolShed Installation Question

Martin Čech
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 the repositories.

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 installed.

Please let us know if you have more questions.

Thank you for using Galaxy.

Martin

On Mon, Nov 28, 2016 at 11:39 AM Yip, Miu ki <[hidden email]> 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.
/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
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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