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": []}
Hi Ido,
if you are using tool_panel_section_id, the panel section has to exist, otherwise, as you have seen, tools will install outside of the tool panel. Now you mentioned that using tool_panel_section_label also installs tools outside of the tool panel, this should not happen. If you specify both, tool_panel_section_id will take precedence. If that is not the case, can you open an issue on https://github.com/ galaxyproject/ephemeris ? The underlying script has moved there, and we will update the anisble-galaxy -tools role to depend on ephemeris shortly.
Best, Marius
On 18 August 2016 at 14:00, Tamir,Ido Ido.Tamir@vbcf.ac.at wrote:
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": []} ___________________________________________________________ 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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It works now! I changed
a) galaxy_tools_base_dir to my galaxy base dir in main.yml b) all {{ galaxy_tools_base_dir }}/venv/bin/python to {{ galaxy_tools_base_dir }}/.venv/bin/python
best, ido
On 18 Aug 2016, at 15:36, Marius van den Beek m.vandenbeek@gmail.com wrote:
Hi Ido,
if you are using tool_panel_section_id, the panel section has to exist, otherwise, as you have seen, tools will install outside of the tool panel. Now you mentioned that using tool_panel_section_label also installs tools outside of the tool panel, this should not happen. If you specify both, tool_panel_section_id will take precedence. If that is not the case, can you open an issue on https://github.com/galaxyproject/ephemeris ? The underlying script has moved there, and we will update the anisble-galaxy-tools role to depend on ephemeris shortly.
Best, Marius
On 18 August 2016 at 14:00, Tamir,Ido Ido.Tamir@vbcf.ac.at wrote: 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": []} ___________________________________________________________ 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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