Docker ToolShed Imports Issue
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
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<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 ___________________________________________________________ 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/
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participants (2)
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Björn Grüning -
Yip, Miu ki