Hi Miuki,
can you please show use your tool.yaml file?
Thanks,
Bjoern
Am 18.08.2016 um 16:31 schrieb Yip, Miu ki:
> Hi all,
>
> I’m trying to import shed tools into Galaxy for Docker. When I build the
> container, I get this error message:
>
> TASK [galaxy_tools : Install Tool Shed tools]
> **
> [WARNING]: The loop variable 'item' is already in use. You should set the
> `loop_var` value in the `loop_control` option for the task to something else
> to
> avoid variable collisions and unexpected behavior.
> failed: [localhost] (item={u'owner': u'vlefort', u'tool_shed_url':
> u'https://toolshed.g2.bx.psu.edu',
> u'tool_panel_section_label': u'Import Files', u'name': u'phyml'}) =>
> {"changed": false, "cmd": ["/tmp/venv/bin/python",
> "install_tool_shed_tools.py", "-y", "name: phyml\nowner:
> vlefort\ntool_panel_section_label: Import Files\ntool_shed_url:
> https://toolshed.g2.bx.psu.edu\n;, "-a", "admin", "-g", "localhost:8080"],
> "delta": "0:00:00.781449", "end": "2016-08-17 23:48:07.389199", "failed":
> true, "failed_when_result": true, "item": {"name": "phyml", "owner":
> "vlefort", "tool_panel_section_label": "Import Files", "tool_shed_url":
> "https://toolshed.g2.bx.psu.edu"}, "rc": 0, "start": "2016-08-17
> 23:48:06.607750", "stderr": "(1/1) Installing tool phyml from vlefort to
> section \"Import Files\" at revision f6dadc1de75f (TRT:
> 0:00:00.308611)\r\n\t* Error installing a tool (after phyml)! Name:
> 0:00:00.247213,owner: vlefort, revision: f6dadc1de75f, error: {\"err_msg\":
> \"Missing required parameter 'shed_tool_conf'.\", \"err_code\":
> 47}\r\nInstalled tools (0): []\r\nSkipped tools (0): []\r\nErrored tools
> (1): [('phyml', u'f6dadc1de75f')]\r\nAll tools listed in 'None' have been
> processed.\r\nTotal run time: 0:00:00.556216", "stdout": "", "stdout_lines":
> [], "warnings": []}
> …ignoring
>
> Is this a conf file issue?
>
> Best,
> Miuki
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