workflow4metabolomics / w4m-vm

Virtual machine for Workflow4Metabolomics Galaxy platform.
http://workflow4metabolomics.org/
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Meeting errors when building vm development version on macOS #20

Open pkrog opened 7 years ago

pkrog commented 7 years ago
     [exec] RUNNING HANDLER [../roles/ansible-galaxy-tools : Check if Galaxy is managed by supervisor] ***
     [exec] fatal: [default]: FAILED! => {"changed": false, "failed": true, "module_stderr": "sudo: a password is required\n", "module_stdout": "", "msg": "MODULE FAILURE"}
     [exec] ...ignoring
     [exec] RUNNING HANDLER [../roles/ansible-galaxy-tools : Restart Galaxy in docker container] ***
     [exec] fatal: [default]: FAILED! => {"changed": true, "cmd": ["docker", "exec", "galaxy", "supervisorctl", "restart", "galaxy:"], "delta": "0:00:00.020628", "end": "2017-02-08 08:40:43.185843", "failed": true, "rc": 1, "start": "2017-02-08 08:40:43.165215", "stderr": "Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?", "stdout": "", "stdout_lines": [], "warnings": []}
pkrog commented 7 years ago

Stop installing tools using Ansible Galaxy role.

lecorguille commented 7 years ago

Hum?

pkrog commented 7 years ago

If you have a solution... What is this "Restart Galaxy in docker container" about?

bgruening commented 7 years ago

The VM is probably misconfigured. Galaxy tries to restart, because of newly installed tools and issues the restart command docker exec ... but this does not work. Maybe because you need to use sudo?

Ansible is by far the most reproducible and stable solution we have currently to install tools. Let me know if you need help here.

W4M is working great on our server also with the ansible roles - so thanks for this great work!

pkrog commented 7 years ago

Retrying again the build of the VM with all tools.

fatal: [default]: FAILED! => {"changed": false, "failed": true, "module_stderr": "sudo: a password is required\n", "module_stdout": "", "msg": "MODULE FAILURE"}
...ignoring
fatal: [default]: FAILED! => {"changed": false, "failed": true, "module_stderr": "sudo: a password is required\n", "module_stdout": "", "msg": "MODULE FAILURE"}
...ignoring
fatal: [default]: FAILED! => {"changed": false, "failed": true, "module_stderr": "sudo: a password is required\n", "module_stdout": "", "msg": "MODULE FAILURE"}
...ignoring
fatal: [default]: FAILED! => {"changed": false, "failed": true, "module_stderr": "sudo: a password is required\n", "module_stdout": "", "msg": "MODULE FAILURE"}
...ignoring
fatal: [default]: FAILED! => {"changed": false, "failed": true, "module_stderr": "sudo: a password is required\n", "module_stdout": "", "msg": "MODULE FAILURE"}
...ignoring
fatal: [default]: FAILED! => {"changed": false, "failed": true, "module_stderr": "sudo: a password is required\n", "module_stdout": "", "msg": "MODULE FAILURE"}
...ignoring
fatal: [default]: FAILED! => {"changed": false, "failed": true, "module_stderr": "sudo: a password is required\n", "module_stdout": "", "msg": "MODULE FAILURE"}
...ignoring
fatal: [default]: FAILED! => {"changed": false, "failed": true, "module_stderr": "sudo: a password is required\n", "module_stdout": "", "msg": "MODULE FAILURE"}
...ignoring
fatal: [default]: FAILED! => {"changed": false, "failed": true, "module_stderr": "sudo: a password is required\n", "module_stdout": "", "msg": "MODULE FAILURE"}
...ignoring
fatal: [default]: FAILED! => {"changed": false, "failed": true, "module_stderr": "sudo: a password is required\n", "module_stdout": "", "msg": "MODULE FAILURE"}
...ignoring
fatal: [default]: FAILED! => {"changed": false, "failed": true, "module_stderr": "sudo: a password is required\n", "module_stdout": "", "msg": "MODULE FAILURE"}
...ignoring

RUNNING HANDLER [../roles/ansible-galaxy-tools : Restart Galaxy in docker container] ***
fatal: [default]: FAILED! => {"changed": true, "cmd": ["docker", "exec", "galaxy", "supervisorctl", "restart", "galaxy:"], "delta": "0:00:00.018122", "end": "2017-03-26 23:32:22.568430", "failed": true, "rc": 1, "start": "2017-03-26 23:32:22.550308", "stderr": "Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?", "stdout": "", "stdout_lines": [], "warnings": []}
fatal: [default]: FAILED! => {"changed": true, "cmd": ["docker", "exec", "galaxy", "supervisorctl", "restart", "galaxy:"], "delta": "0:00:00.018930", "end": "2017-03-26 23:32:22.334452", "failed": true, "rc": 1, "start": "2017-03-26 23:32:22.315522", "stderr": "Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?", "stdout": "", "stdout_lines": [], "warnings": []}
fatal: [default]: FAILED! => {"changed": true, "cmd": ["docker", "exec", "galaxy", "supervisorctl", "restart", "galaxy:"], "delta": "0:00:00.018475", "end": "2017-03-26 23:32:22.096605", "failed": true, "rc": 1, "start": "2017-03-26 23:32:22.078130", "stderr": "Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?", "stdout": "", "stdout_lines": [], "warnings": []}
fatal: [default]: FAILED! => {"changed": true, "cmd": ["docker", "exec", "galaxy", "supervisorctl", "restart", "galaxy:"], "delta": "0:00:00.017791", "end": "2017-03-26 23:32:21.856237", "failed": true, "rc": 1, "start": "2017-03-26 23:32:21.838446", "stderr": "Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?", "stdout": "", "stdout_lines": [], "warnings": []}
fatal: [default]: FAILED! => {"changed": true, "cmd": ["docker", "exec", "galaxy", "supervisorctl", "restart", "galaxy:"], "delta": "0:00:00.022046", "end": "2017-03-26 23:32:21.582829", "failed": true, "rc": 1, "start": "2017-03-26 23:32:21.560783", "stderr": "Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?", "stdout": "", "stdout_lines": [], "warnings": []}
fatal: [default]: FAILED! => {"changed": true, "cmd": ["docker", "exec", "galaxy", "supervisorctl", "restart", "galaxy:"], "delta": "0:00:00.019834", "end": "2017-03-26 23:32:21.297245", "failed": true, "rc": 1, "start": "2017-03-26 23:32:21.277411", "stderr": "Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?", "stdout": "", "stdout_lines": [], "warnings": []}
fatal: [default]: FAILED! => {"changed": true, "cmd": ["docker", "exec", "galaxy", "supervisorctl", "restart", "galaxy:"], "delta": "0:00:00.021505", "end": "2017-03-26 23:32:21.014588", "failed": true, "rc": 1, "start": "2017-03-26 23:32:20.993083", "stderr": "Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?", "stdout": "", "stdout_lines": [], "warnings": []}
fatal: [default]: FAILED! => {"changed": true, "cmd": ["docker", "exec", "galaxy", "supervisorctl", "restart", "galaxy:"], "delta": "0:00:00.018196", "end": "2017-03-26 23:32:20.755966", "failed": true, "rc": 1, "start": "2017-03-26 23:32:20.737770", "stderr": "Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?", "stdout": "", "stdout_lines": [], "warnings": []}
fatal: [default]: FAILED! => {"changed": true, "cmd": ["docker", "exec", "galaxy", "supervisorctl", "restart", "galaxy:"], "delta": "0:00:00.019824", "end": "2017-03-26 23:32:20.467393", "failed": true, "rc": 1, "start": "2017-03-26 23:32:20.447569", "stderr": "Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?", "stdout": "", "stdout_lines": [], "warnings": []}
fatal: [default]: FAILED! => {"changed": true, "cmd": ["docker", "exec", "galaxy", "supervisorctl", "restart", "galaxy:"], "delta": "0:00:00.522594", "end": "2017-03-26 23:32:20.197734", "failed": true, "rc": 1, "start": "2017-03-26 23:32:19.675140", "stderr": "Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?", "stdout": "", "stdout_lines": [], "warnings": []}
fatal: [default]: FAILED! => {"changed": true, "cmd": ["docker", "exec", "galaxy", "supervisorctl", "restart", "galaxy:"], "delta": "0:00:00.017371", "end": "2017-03-26 23:32:22.802992", "failed": true, "rc": 1, "start": "2017-03-26 23:32:22.785621", "stderr": "Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?", "stdout": "", "stdout_lines": [], "warnings": []}

RUNNING HANDLER [../roles/ansible-galaxy-tools : Stop Galaxy] ******************

RUNNING HANDLER [../roles/ansible-galaxy-tools : Wait for Galaxy to stop] ******

RUNNING HANDLER [../roles/ansible-galaxy-tools : Start Galaxy] *****************

RUNNING HANDLER [../roles/ansible-galaxy-tools : Wait for Galaxy to start] *****

RUNNING HANDLER [../roles/ansible-galaxy-tools : Restart Galaxy] ***************

RUNNING HANDLER [../roles/ansible-galaxy-tools : pause] ************************
        to retry, use: --limit @/Users/pierrick/dev/w4m-vm/tools.retry

PLAY RECAP *********************************************************************
default                    : ok=15   changed=1    unreachable=0    failed=11
pkrog commented 7 years ago

It is stranged that a password be required. The installation is made with user vagrant, which has sudo access rights without password.

bgruening commented 7 years ago

How do you invoke docker with or without sudo?

pkrog commented 7 years ago

Well, I don't invoke docker directly, and I don't understand why Galaxy installation is trying to invoke it. The installation of Galaxy is made with Ansible using the file galaxyserver.yml as user vagrant. The installation of the tools using one of the YAML files in submodule w4m-config, still as user vagrant.

Is the installation of docker not a standard (by default) feature in Galaxy?