Question

Question: Galaxy: Error when Installing tools with Ansible playbook for the Galaxy Tools

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2.0 years ago by

termanini • 10 wrote:

Hello, I am trying to install tools automatically by using Ansible and Ansible playbook for the Galaxy Tools role as described here: https://github.com/afgane/galaxy-tools-playbook

While I can install tools via the Galaxy web interface, when running the installation with Ansible I got an error after running:

ansible-playbook tools.yml -i "localhost," --extra-vars galaxy_tools_api_key=mykeyblablabla

TASK [galaxyprojectdotorg.galaxy-tools : Install Tool Shed tools] **** failed

Below are the config files and the complete output. Could anyone help me? I am trying to solve this problem from a long time. Thanks very much!

Best, Albert

The requirement_roles.yml file contains: - src: https://github.com/galaxyproject/ansible-galaxy-tools.git name: galaxyprojectdotorg.galaxy-tools

The tools.yml file contains: - hosts: localhost gather_facts: False connection: local vars: galaxy_tools_tool_list_files: [ "files/tool_list.yaml" ] galaxy_tools_galaxy_instance_url: http://127.0.0.1:8080/ # galaxy_tools_api_key: <api key="" for="" galaxy="" admin="" user=""> roles: - galaxyprojectdotorg.galaxy-tools

The files/tool_list.yaml file contains: tools: - name: 'tophat2' owner: 'devteam' tool_panel_section_id: 'alignments' revisions: - '758594ed0364' # rev 8

This is the output is:

PLAY [localhost] *********************

TASK [galaxyprojectdotorg.galaxy-tools : fail] *********** skipping: [localhost]

TASK [galaxyprojectdotorg.galaxy-tools : Copy the bootstrap user management script] * skipping: [localhost]

TASK [galaxyprojectdotorg.galaxy-tools : Create Galaxy bootstrap user] *** skipping: [localhost]

TASK [galaxyprojectdotorg.galaxy-tools : Check/Set bootstrap user as Galaxy Admin if admin_users tag is already in the config file] * skipping: [localhost]

TASK [galaxyprojectdotorg.galaxy-tools : Set bootstrap user as Galaxy Admin] * skipping: [localhost]

TASK [galaxyprojectdotorg.galaxy-tools : Delete Galaxy bootstrap user] *** skipping: [localhost]

TASK [galaxyprojectdotorg.galaxy-tools : Remove bootstrap user as Galaxy Admin if admin_users tag was already in the config file before bootstrap_user task] * skipping: [localhost]

TASK [galaxyprojectdotorg.galaxy-tools : Remove bootstrap user as Galaxy Admin] skipping: [localhost]

TASK [galaxyprojectdotorg.galaxy-tools : Remove the bootstrap user management script] * skipping: [localhost]

TASK [galaxyprojectdotorg.galaxy-tools : set_fact] ********* skipping: [localhost]

TASK [galaxyprojectdotorg.galaxy-tools : Create/invoke script virtualenv] ** ok: [localhost] => (item=ephemeris==0.4.0)

TASK [galaxyprojectdotorg.galaxy-tools : include] ********** included: /home/ec2-user/galaxy-tools-playbook/roles/galaxyprojectdotorg.galaxy-tools/tasks/install_tool_list.yml for localhost

TASK [galaxyprojectdotorg.galaxy-tools : get tool list] ******** ok: [localhost]

TASK [galaxyprojectdotorg.galaxy-tools : Install Tool Shed tools] **** failed: [localhost] (item={u'owner': u'devteam', u'tool_panel_section_id': u'textutil', u'name': u'column_maker', u'revisions': [u'08a01b2ce4cd']}) => {"changed": false, "cmd": ["/tmp/venv/bin/shed-install", "-y", "name: column_maker\nowner: devteam\nrevisions:\n- 08a01b2ce4cd\ntool_panel_section_id: textutil\n", "-a", "f223219a533359d1c3fb53b7ae2aa15b", "-g", "http://127.0.0.1:8080/"], "delta": "0:00:00.108436", "end": "2016-11-21 05:43:20.001232", "failed": true, "failed_when_result": true, "item": {"name": "column_maker", "owner": "devteam", "revisions": ["08a01b2ce4cd"], "tool_panel_section_id": "textutil"}, "rc": 1, "start": "2016-11-21 05:43:19.892796", "stderr": "Traceback (most recent call last):\n File \"/tmp/venv/bin/shed-install\", line 11, in <module>\n sys.exit(script_main())\n File \"/tmp/venv/lib/python2.7/site-packages/ephemeris/shed_install.py\", line 720, in script_main\n itm.install_tools()\n File \"/tmp/venv/lib/python2.7/site-packages/ephemeris/shed_install.py\", line 592, in install_tools\n itl = installed_tool_revisionsself.gi) # installed tools list\n File \"/tmp/venv/lib/python2.7/site-packages/ephemeris/shed_install.py\", line 219, in installed_tool_revisions\n itl = tsc.get_repositories()\n File \"/tmp/venv/lib/python2.7/site-packages/bioblend/galaxy/toolshed/__init__.py\", line 36, in get_repositories\n return Client._get(self)\n File \"/tmp/venv/lib/python2.7/site-packages/bioblend/galaxy/client.py\", line 132, in _get\n raise ConnectionError(msg, body=r.text,\n File \"/tmp/venv/lib/python2.7/site-packages/requests/models.py\", line 796, in text\n if not self.content:\n File \"/tmp/venv/lib/python2.7/site-packages/requests/models.py\", line 772, in content\n self._content = bytes().join(self.iter_content(CONTENT_CHUNK_SIZE)) or bytes()\n File \"/tmp/venv/lib/python2.7/site-packages/requests/models.py\", line 705, in generate\n chunk = self.raw.read(chunk_size)\nAttributeError: 'NoneType' object has no attribute 'read'", "stdout": "", "stdout_lines": [], "warnings": []}

[MANY OTHERS]

...ignoring

TASK [galaxyprojectdotorg.galaxy-tools : Create/invoke script virtualenv] ** skipping: [localhost] => (item=pyyaml) skipping: [localhost] => (item=bioblend)

TASK [galaxyprojectdotorg.galaxy-tools : Place the tool management script] * skipping: [localhost]

TASK [galaxyprojectdotorg.galaxy-tools : Copy workflows] *******

TASK [galaxyprojectdotorg.galaxy-tools : Install workflows] ******

TASK [galaxyprojectdotorg.galaxy-tools : Remove workflow script] ***** skipping: [localhost]