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<http://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\": 400007}\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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