Hi, I am trying to install tools with the galaxy-tools-playbook, but my tools don’t end up in the sections. I added section test in tool_conf.xml and test2 in shed_tool_conf.xml, and after a restart they are together in integrated_tool_panel.xml.
<section id="test" name="test section" version=""> </section> <section id="test2" name="test section 2" version=""> </section>
Then I started the ansible playbook with these entries: - name: 'drop_column' owner: 'brigidar' tool_panel_section_id: 'test' - name: 'transpose' owner: 'jmsong' tool_panel_section_id: ‘test2'
The install did work, but the tools don’t end up in the sections. I also tried the tool_panel_section_label (without having the label defined in any .xml), and this also placed the tools outside of the sections.
ansible log output:
ok: [localhost] => {"ansible_facts": {"tools": [{"name": "cutadapt", "owner": "lparsons", "tool_panel_section_id": "ngs_cutadapt"}, {"name": "drop_column", "owner": "brigidar", "tool_panel_section_id": "test"}, {"name": "map_chromosomes", "owner": "pmac", "tool_panel_section_id": "test2"}]}, "changed": false, "invocation": {"module_args": {"_raw_params": "files/vbcf_tool_list.yaml"}, "module_name": "include_vars"}}
changed: [localhost] => (item={u'owner': u'brigidar', u'tool_panel_section_id': u'test', u'name': u'drop_column'}) => {"changed": true, "cmd": ["/tmp/venv/bin/python", "install_tool_shed_tools.py", "-y", "name: drop_column\nowner: brigidar\ntool_panel_section_id: test\n", "-a", "7e7c8ec27a0a99acee883d2beea8a60b", "-g", "http://127.0.0.1:9090/"], "delta": "0:00:09.867642", "end": "2016-08-18 13:19:07.389878", "failed": false, "failed_when_result": false, "invocation": {"module_args": {"_raw_params": "/tmp/venv/bin/python install_tool_shed_tools.py -y "name: drop_column\nowner: brigidar\ntool_panel_section_id: test\n" -a 7e7c8ec27a0a99acee883d2beea8a60b -g http://127.0.0.1:9090/", "_uses_shell": false, "chdir": "/tmp", "creates": null, "executable": null, "removes": null, "warn": true}, "module_name": "command"}, "item": {"name": "drop_column", "owner": "brigidar", "tool_panel_section_id": "test"}, "rc": 0, "start": "2016-08-18 13:18:57.522236", "stderr": "(1/1) Installing tool drop_column from brigidar to section "test" at revision befa27962b5e (TRT: 0:00:00.996404)\r\n\tTool drop_column installed successfully (in 0:00:08.505926) at revision befa27962b5e\r\nInstalled tools (1): [('drop_column', u'befa27962b5e')]\r\nSkipped tools (0): []\r\nErrored tools (0): []\r\nAll tools listed in 'None' have been processed.\r\nTotal run time: 0:00:09.502762", "stdout": "", "stdout_lines": [], "warnings": []}
changed: [localhost] => (item={u'owner': u'pmac', u'tool_panel_section_id': u'test2', u'name': u'map_chromosomes'}) => {"changed": true, "cmd": ["/tmp/venv/bin/python", "install_tool_shed_tools.py", "-y", "name: map_chromosomes\nowner: pmac\ntool_panel_section_id: test2\n", "-a", "7e7c8ec27a0a99acee883d2beea8a60b", "-g", "http://127.0.0.1:9090/"], "delta": "0:00:08.982071", "end": "2016-08-18 13:19:17.786115", "failed": false, "failed_when_result": false, "invocation": {"module_args": {"_raw_params": "/tmp/venv/bin/python install_tool_shed_tools.py -y "name: map_chromosomes\nowner: pmac\ntool_panel_section_id: test2\n" -a 7e7c8ec27a0a99acee883d2beea8a60b -g http://127.0.0.1:9090/", "_uses_shell": false, "chdir": "/tmp", "creates": null, "executable": null, "removes": null, "warn": true}, "module_name": "command"}, "item": {"name": "map_chromosomes", "owner": "pmac", "tool_panel_section_id": "test2"}, "rc": 0, "start": "2016-08-18 13:19:08.804044", "stderr": "(1/1) Installing tool map_chromosomes from pmac to section "test2" at revision e60f92a8e1c8 (TRT: 0:00:01.040988)\r\n\tTool map_chromosomes installed successfully (in 0:00:07.576596) at revision e60f92a8e1c8\r\nInstalled tools (1): [('map_chromosomes', u'e60f92a8e1c8')]\r\nSkipped tools (0): []\r\nErrored tools (0): []\r\nAll tools listed in 'None' have been processed.\r\nTotal run time: 0:00:08.618238", "stdout": "", "stdout_lines": [], "warnings": []}