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Created August 22, 2022 23:38
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systemd not writeable error
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20220822_1937.txt
(base) [vgl_galaxy@vglgalaxy /lustre/fs5/vgl/scratch/vgl_galaxy/galaxy]$ ansible-playbook galaxy.yml -u $USER
PLAY [galaxyservers] ***********************************************************************************************************************************************************
TASK [Gathering Facts] *********************************************************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [Install Dependencies] ****************************************************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [natefoo.postgresql_objects : Revoke extra privileges] ********************************************************************************************************************
TASK [natefoo.postgresql_objects : Drop databases] *****************************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu] => (item={'name': 'galaxy', 'owner': 'galaxy'})
TASK [natefoo.postgresql_objects : Create and drop users] **********************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu] => (item={'name': 'galaxy'})
TASK [natefoo.postgresql_objects : Create groups] ******************************************************************************************************************************
TASK [natefoo.postgresql_objects : Add or remove users from groups] ************************************************************************************************************
TASK [natefoo.postgresql_objects : Drop groups] ********************************************************************************************************************************
TASK [natefoo.postgresql_objects : Create databases] ***************************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu] => (item={'name': 'galaxy', 'owner': 'galaxy'})
TASK [natefoo.postgresql_objects : Grant user database privileges] *************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu] => (item={'name': 'galaxy'})
TASK [natefoo.postgresql_objects : Grant extra privileges] *********************************************************************************************************************
TASK [geerlingguy.pip : Ensure Pip is installed.] ******************************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [geerlingguy.pip : Ensure pip_install_packages are installed.] ************************************************************************************************************
TASK [galaxyproject.galaxy : Ensure that mutually exclusive options are not set] ***********************************************************************************************
ok: [vglgalaxy.rockefeller.edu] => {
"changed": false,
"msg": "All assertions passed"
}
TASK [galaxyproject.galaxy : Set privilege separation default variables] *******************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include layout vars] ******************************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Set any unset variables from layout defaults] *****************************************************************************************************
ok: [vglgalaxy.rockefeller.edu] => (item=galaxy_venv_dir)
ok: [vglgalaxy.rockefeller.edu] => (item=galaxy_server_dir)
ok: [vglgalaxy.rockefeller.edu] => (item=galaxy_config_dir)
ok: [vglgalaxy.rockefeller.edu] => (item=galaxy_mutable_data_dir)
ok: [vglgalaxy.rockefeller.edu] => (item=galaxy_mutable_config_dir)
ok: [vglgalaxy.rockefeller.edu] => (item=galaxy_shed_tools_dir)
ok: [vglgalaxy.rockefeller.edu] => (item=galaxy_cache_dir)
ok: [vglgalaxy.rockefeller.edu] => (item=galaxy_local_tools_dir)
TASK [galaxyproject.galaxy : Check that any explicitly set Galaxy config options match the values of explicitly set variables] *************************************************
skipping: [vglgalaxy.rockefeller.edu] => (item=tool_dependency_dir)
skipping: [vglgalaxy.rockefeller.edu] => (item=file_path)
skipping: [vglgalaxy.rockefeller.edu] => (item=job_working_directory)
skipping: [vglgalaxy.rockefeller.edu] => (item=shed_tool_config_file)
TASK [galaxyproject.galaxy : Set any unset variables corresponding to Galaxy config options from galaxy_config or layout defaults] *********************************************
ok: [vglgalaxy.rockefeller.edu] => (item=tool_dependency_dir)
ok: [vglgalaxy.rockefeller.edu] => (item=file_path)
ok: [vglgalaxy.rockefeller.edu] => (item=job_working_directory)
TASK [galaxyproject.galaxy : Include user creation tasks] **********************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include path management tasks] ********************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include clone tasks] ******************************************************************************************************************************
included: /lustre/fs5/vgl/scratch/vgl_galaxy/galaxy/roles/galaxyproject.galaxy/tasks/clone.yml for vglgalaxy.rockefeller.edu
TASK [galaxyproject.galaxy : Update Galaxy to specified ref] *******************************************************************************************************************
changed: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Report Galaxy version change] *********************************************************************************************************************
changed: [vglgalaxy.rockefeller.edu] => {
"msg": "Galaxy version changed from '0a69d3d8822f4863648e3137e2d63fcf9b6c5ff5' to '0a69d3d8822f4863648e3137e2d63fcf9b6c5ff5'"
}
TASK [galaxyproject.galaxy : Create Galaxy virtualenv] *************************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Ensure pip and setuptools are the latest release] *************************************************************************************************
changed: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Remove orphaned .pyc files and compile bytecode] **************************************************************************************************
changed: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include download tasks] ***************************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include manage existing galaxy tasks] *************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include static config setup tasks] ****************************************************************************************************************
included: /lustre/fs5/vgl/scratch/vgl_galaxy/galaxy/roles/galaxyproject.galaxy/tasks/static_setup.yml for vglgalaxy.rockefeller.edu
TASK [galaxyproject.galaxy : Ensure Galaxy version is set] *********************************************************************************************************************
included: /lustre/fs5/vgl/scratch/vgl_galaxy/galaxy/roles/galaxyproject.galaxy/tasks/_inc_galaxy_version.yml for vglgalaxy.rockefeller.edu
TASK [galaxyproject.galaxy : Collect Galaxy version file] **********************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Determine Galaxy version] *************************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Install additional Galaxy config files (static)] **************************************************************************************************
TASK [galaxyproject.galaxy : Install additional Galaxy config files (template)] ************************************************************************************************
TASK [galaxyproject.galaxy : Install local tools] ******************************************************************************************************************************
TASK [galaxyproject.galaxy : Install local_tool_conf.xml] **********************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Append local_tool_conf.xml to tool_config_file Galaxy config option] ******************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Append shed_tool_conf.xml to tool_config_file Galaxy config option] *******************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Ensure dynamic job rules paths exists] ************************************************************************************************************
TASK [galaxyproject.galaxy : Install dynamic job rules] ************************************************************************************************************************
TASK [galaxyproject.galaxy : Ensure dynamic rule __init__.py's exist] **********************************************************************************************************
TASK [galaxyproject.galaxy : Create Galaxy job metrics configuration file] *****************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Create Galaxy dependency resolvers configuration file] ********************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Create Galaxy container resolvers configuration file] *********************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Create Galaxy configuration file] *****************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include dependency setup tasks] *******************************************************************************************************************
included: /lustre/fs5/vgl/scratch/vgl_galaxy/galaxy/roles/galaxyproject.galaxy/tasks/dependencies.yml for vglgalaxy.rockefeller.edu
TASK [galaxyproject.galaxy : Create Galaxy virtualenv] *************************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Ensure pip and setuptools are the latest release] *************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Install Galaxy base dependencies] *****************************************************************************************************************
changed: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Collect Galaxy conditional dependency requirement strings] ****************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Install Galaxy conditional dependencies] **********************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include mutable config setup tasks] ***************************************************************************************************************
included: /lustre/fs5/vgl/scratch/vgl_galaxy/galaxy/roles/galaxyproject.galaxy/tasks/mutable_setup.yml for vglgalaxy.rockefeller.edu
TASK [galaxyproject.galaxy : Ensure Galaxy version is set] *********************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Instantiate mutable configuration files] **********************************************************************************************************
ok: [vglgalaxy.rockefeller.edu] => (item={'src': 'shed_data_manager_conf.xml', 'dest': '/lustre/fs5/vgl/scratch/vgl_galaxy/galaxy_srv//var/config/shed_data_manager_conf.xml'})
ok: [vglgalaxy.rockefeller.edu] => (item={'src': 'shed_tool_data_table_conf.xml', 'dest': '/lustre/fs5/vgl/scratch/vgl_galaxy/galaxy_srv//var/config/shed_tool_data_table_conf.xml'})
TASK [galaxyproject.galaxy : Instantiate mutable configuration templates] ******************************************************************************************************
ok: [vglgalaxy.rockefeller.edu] => (item={'src': 'shed_tool_conf.xml.j2', 'dest': '/lustre/fs5/vgl/scratch/vgl_galaxy/galaxy_srv//var/config/migrated_tools_conf.xml'})
ok: [vglgalaxy.rockefeller.edu] => (item={'src': 'shed_tool_conf.xml.j2', 'dest': '/lustre/fs5/vgl/scratch/vgl_galaxy/galaxy_srv//var/config/shed_tool_conf.xml'})
TASK [galaxyproject.galaxy : Include database management tasks] ****************************************************************************************************************
included: /lustre/fs5/vgl/scratch/vgl_galaxy/galaxy/roles/galaxyproject.galaxy/tasks/database.yml for vglgalaxy.rockefeller.edu
TASK [galaxyproject.galaxy : Get current Galaxy DB version] ********************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Get maximum Galaxy DB version] ********************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Report current and max Galaxy database] ***********************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Upgrade Galaxy DB] ********************************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include client build tasks] ***********************************************************************************************************************
included: /lustre/fs5/vgl/scratch/vgl_galaxy/galaxy/roles/galaxyproject.galaxy/tasks/client.yml for vglgalaxy.rockefeller.edu
TASK [galaxyproject.galaxy : Ensure client_build_hash.txt exists] **************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Get current client commit id] *********************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Check if Galaxy was checked out from git] *********************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Get current Galaxy commit id] *********************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Set client build version fact] ********************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Set client build version fact] ********************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Report client version mismatch] *******************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Ensure galaxy_node_version is set] ****************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Install node] *************************************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Install yarn] *************************************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include client build process] *********************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include error document setup tasks] ***************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include systemd unit setup tasks (Mules)] *********************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include systemd unit setup tasks (Reports)] *******************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
RUNNING HANDLER [galaxyproject.galaxy : default restart galaxy handler] ********************************************************************************************************
ok: [vglgalaxy.rockefeller.edu] => {
"msg": "RESTARTER NOT IMPLEMENTED - Please restart Galaxy manually. You can define your own handler and enable it with `galaxy_restart_handler_name`"
}
RUNNING HANDLER [galaxyproject.galaxy : email administrator with commit id] ****************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
PLAY RECAP *********************************************************************************************************************************************************************
vglgalaxy.rockefeller.edu : ok=41 changed=5 unreachable=0 failed=0 skipped=37 rescued=0 ignored=0
(base) [vgl_galaxy@vglgalaxy /lustre/fs5/vgl/scratch/vgl_galaxy/galaxy]$ vim group_vars/galaxyservers.yml
(base) [vgl_galaxy@vglgalaxy /lustre/fs5/vgl/scratch/vgl_galaxy/galaxy]$ ansible-playbook galaxy.yml -u $USER
PLAY [galaxyservers] ***********************************************************************************************************************************************************
TASK [Gathering Facts] *********************************************************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [Install Dependencies] ****************************************************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [natefoo.postgresql_objects : Revoke extra privileges] ********************************************************************************************************************
TASK [natefoo.postgresql_objects : Drop databases] *****************************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu] => (item={'name': 'galaxy', 'owner': 'galaxy'})
TASK [natefoo.postgresql_objects : Create and drop users] **********************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu] => (item={'name': 'galaxy'})
TASK [natefoo.postgresql_objects : Create groups] ******************************************************************************************************************************
TASK [natefoo.postgresql_objects : Add or remove users from groups] ************************************************************************************************************
TASK [natefoo.postgresql_objects : Drop groups] ********************************************************************************************************************************
TASK [natefoo.postgresql_objects : Create databases] ***************************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu] => (item={'name': 'galaxy', 'owner': 'galaxy'})
TASK [natefoo.postgresql_objects : Grant user database privileges] *************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu] => (item={'name': 'galaxy'})
TASK [natefoo.postgresql_objects : Grant extra privileges] *********************************************************************************************************************
TASK [geerlingguy.pip : Ensure Pip is installed.] ******************************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [geerlingguy.pip : Ensure pip_install_packages are installed.] ************************************************************************************************************
TASK [galaxyproject.galaxy : Ensure that mutually exclusive options are not set] ***********************************************************************************************
ok: [vglgalaxy.rockefeller.edu] => {
"changed": false,
"msg": "All assertions passed"
}
TASK [galaxyproject.galaxy : Set privilege separation default variables] *******************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include layout vars] ******************************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Set any unset variables from layout defaults] *****************************************************************************************************
ok: [vglgalaxy.rockefeller.edu] => (item=galaxy_venv_dir)
ok: [vglgalaxy.rockefeller.edu] => (item=galaxy_server_dir)
ok: [vglgalaxy.rockefeller.edu] => (item=galaxy_config_dir)
ok: [vglgalaxy.rockefeller.edu] => (item=galaxy_mutable_data_dir)
ok: [vglgalaxy.rockefeller.edu] => (item=galaxy_mutable_config_dir)
ok: [vglgalaxy.rockefeller.edu] => (item=galaxy_shed_tools_dir)
ok: [vglgalaxy.rockefeller.edu] => (item=galaxy_cache_dir)
ok: [vglgalaxy.rockefeller.edu] => (item=galaxy_local_tools_dir)
TASK [galaxyproject.galaxy : Check that any explicitly set Galaxy config options match the values of explicitly set variables] *************************************************
skipping: [vglgalaxy.rockefeller.edu] => (item=tool_dependency_dir)
skipping: [vglgalaxy.rockefeller.edu] => (item=file_path)
skipping: [vglgalaxy.rockefeller.edu] => (item=job_working_directory)
skipping: [vglgalaxy.rockefeller.edu] => (item=shed_tool_config_file)
TASK [galaxyproject.galaxy : Set any unset variables corresponding to Galaxy config options from galaxy_config or layout defaults] *********************************************
ok: [vglgalaxy.rockefeller.edu] => (item=tool_dependency_dir)
ok: [vglgalaxy.rockefeller.edu] => (item=file_path)
ok: [vglgalaxy.rockefeller.edu] => (item=job_working_directory)
TASK [galaxyproject.galaxy : Include user creation tasks] **********************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include path management tasks] ********************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include clone tasks] ******************************************************************************************************************************
included: /lustre/fs5/vgl/scratch/vgl_galaxy/galaxy/roles/galaxyproject.galaxy/tasks/clone.yml for vglgalaxy.rockefeller.edu
TASK [galaxyproject.galaxy : Update Galaxy to specified ref] *******************************************************************************************************************
changed: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Report Galaxy version change] *********************************************************************************************************************
changed: [vglgalaxy.rockefeller.edu] => {
"msg": "Galaxy version changed from '0a69d3d8822f4863648e3137e2d63fcf9b6c5ff5' to '0a69d3d8822f4863648e3137e2d63fcf9b6c5ff5'"
}
TASK [galaxyproject.galaxy : Create Galaxy virtualenv] *************************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Ensure pip and setuptools are the latest release] *************************************************************************************************
changed: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Remove orphaned .pyc files and compile bytecode] **************************************************************************************************
changed: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include download tasks] ***************************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include manage existing galaxy tasks] *************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include static config setup tasks] ****************************************************************************************************************
included: /lustre/fs5/vgl/scratch/vgl_galaxy/galaxy/roles/galaxyproject.galaxy/tasks/static_setup.yml for vglgalaxy.rockefeller.edu
TASK [galaxyproject.galaxy : Ensure Galaxy version is set] *********************************************************************************************************************
included: /lustre/fs5/vgl/scratch/vgl_galaxy/galaxy/roles/galaxyproject.galaxy/tasks/_inc_galaxy_version.yml for vglgalaxy.rockefeller.edu
TASK [galaxyproject.galaxy : Collect Galaxy version file] **********************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Determine Galaxy version] *************************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Install additional Galaxy config files (static)] **************************************************************************************************
TASK [galaxyproject.galaxy : Install additional Galaxy config files (template)] ************************************************************************************************
TASK [galaxyproject.galaxy : Install local tools] ******************************************************************************************************************************
TASK [galaxyproject.galaxy : Install local_tool_conf.xml] **********************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Append local_tool_conf.xml to tool_config_file Galaxy config option] ******************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Append shed_tool_conf.xml to tool_config_file Galaxy config option] *******************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Ensure dynamic job rules paths exists] ************************************************************************************************************
TASK [galaxyproject.galaxy : Install dynamic job rules] ************************************************************************************************************************
TASK [galaxyproject.galaxy : Ensure dynamic rule __init__.py's exist] **********************************************************************************************************
TASK [galaxyproject.galaxy : Create Galaxy job metrics configuration file] *****************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Create Galaxy dependency resolvers configuration file] ********************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Create Galaxy container resolvers configuration file] *********************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Create Galaxy configuration file] *****************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include dependency setup tasks] *******************************************************************************************************************
included: /lustre/fs5/vgl/scratch/vgl_galaxy/galaxy/roles/galaxyproject.galaxy/tasks/dependencies.yml for vglgalaxy.rockefeller.edu
TASK [galaxyproject.galaxy : Create Galaxy virtualenv] *************************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Ensure pip and setuptools are the latest release] *************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Install Galaxy base dependencies] *****************************************************************************************************************
changed: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Collect Galaxy conditional dependency requirement strings] ****************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Install Galaxy conditional dependencies] **********************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include mutable config setup tasks] ***************************************************************************************************************
included: /lustre/fs5/vgl/scratch/vgl_galaxy/galaxy/roles/galaxyproject.galaxy/tasks/mutable_setup.yml for vglgalaxy.rockefeller.edu
TASK [galaxyproject.galaxy : Ensure Galaxy version is set] *********************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Instantiate mutable configuration files] **********************************************************************************************************
ok: [vglgalaxy.rockefeller.edu] => (item={'src': 'shed_data_manager_conf.xml', 'dest': '/lustre/fs5/vgl/scratch/vgl_galaxy/galaxy_srv//var/config/shed_data_manager_conf.xml'})
ok: [vglgalaxy.rockefeller.edu] => (item={'src': 'shed_tool_data_table_conf.xml', 'dest': '/lustre/fs5/vgl/scratch/vgl_galaxy/galaxy_srv//var/config/shed_tool_data_table_conf.xml'})
TASK [galaxyproject.galaxy : Instantiate mutable configuration templates] ******************************************************************************************************
ok: [vglgalaxy.rockefeller.edu] => (item={'src': 'shed_tool_conf.xml.j2', 'dest': '/lustre/fs5/vgl/scratch/vgl_galaxy/galaxy_srv//var/config/migrated_tools_conf.xml'})
ok: [vglgalaxy.rockefeller.edu] => (item={'src': 'shed_tool_conf.xml.j2', 'dest': '/lustre/fs5/vgl/scratch/vgl_galaxy/galaxy_srv//var/config/shed_tool_conf.xml'})
TASK [galaxyproject.galaxy : Include database management tasks] ****************************************************************************************************************
included: /lustre/fs5/vgl/scratch/vgl_galaxy/galaxy/roles/galaxyproject.galaxy/tasks/database.yml for vglgalaxy.rockefeller.edu
TASK [galaxyproject.galaxy : Get current Galaxy DB version] ********************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Get maximum Galaxy DB version] ********************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Report current and max Galaxy database] ***********************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Upgrade Galaxy DB] ********************************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include client build tasks] ***********************************************************************************************************************
included: /lustre/fs5/vgl/scratch/vgl_galaxy/galaxy/roles/galaxyproject.galaxy/tasks/client.yml for vglgalaxy.rockefeller.edu
TASK [galaxyproject.galaxy : Ensure client_build_hash.txt exists] **************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Get current client commit id] *********************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Check if Galaxy was checked out from git] *********************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Get current Galaxy commit id] *********************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Set client build version fact] ********************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Set client build version fact] ********************************************************************************************************************
ok: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Report client version mismatch] *******************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Ensure galaxy_node_version is set] ****************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Install node] *************************************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Install yarn] *************************************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include client build process] *********************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include error document setup tasks] ***************************************************************************************************************
skipping: [vglgalaxy.rockefeller.edu]
TASK [galaxyproject.galaxy : Include systemd unit setup tasks (Mules)] *********************************************************************************************************
included: /lustre/fs5/vgl/scratch/vgl_galaxy/galaxy/roles/galaxyproject.galaxy/tasks/systemd-mule.yml for vglgalaxy.rockefeller.edu
TASK [galaxyproject.galaxy : Deploy Galaxy Unit] *******************************************************************************************************************************
fatal: [vglgalaxy.rockefeller.edu]: FAILED! => {"changed": false, "checksum": "c8a6b5aa307cef7953a5d3cddedb269a329a9550", "msg": "Destination /etc/systemd/system not writable"}
RUNNING HANDLER [galaxyproject.galaxy : email administrator with commit id] ****************************************************************************************************
RUNNING HANDLER [galaxyproject.galaxy : galaxy mule restart] *******************************************************************************************************************
PLAY RECAP *********************************************************************************************************************************************************************
vglgalaxy.rockefeller.edu : ok=41 changed=5 unreachable=0 failed=1 skipped=34 rescued=0 ignored=0
(base) [vgl_galaxy@vglgalaxy /lustre/fs5/vgl/scratch/vgl_galaxy/galaxy]$ cat group_vars/galaxyservers.yml
---
# Python 3 support
pip_virtualenv_command: /rugpfs/fs0/home/vgl_galaxy/miniconda3/bin/python3 -m virtualenv # usegalaxy_eu.certbot, usegalaxy_eu.tiaas2, galaxyproject.galaxy
certbot_virtualenv_package_name: python3-virtualenv # usegalaxy_eu.certbot
pip_package: python3-pip # geerlingguy.pip
# PostgreSQL
postgresql_objects_users:
- name: galaxy
postgresql_objects_databases:
- name: galaxy
owner: galaxy
postgresql_objects_port: 5432
postgresql_objects_login_host: vglgalaxy.rockefeller.edu
postgresql_objects_login_user: vgl_galaxy
# PostgreSQL Backups
postgresql_backup_dir: /lustre/fs5/vgl/scratch/vgl_galaxy/data/backups
postgresql_backup_local_dir: "{{ '~vgl_galaxy' | expanduser }}/scratch/backups"
# Galaxy
galaxy_create_user: false
galaxy_separate_privileges: false
galaxy_manage_paths: false
galaxy_layout: root-dir
galaxy_root: /lustre/fs5/vgl/scratch/vgl_galaxy/galaxy_srv/
galaxy_user: {name: vgl_galaxy, shell: /bin/bash}
galaxy_privsep_user: {name: vgl_galaxy, shell: /bin/bash}
galaxy_group: {name: vgl_galaxy, shell: /bin/bash}
galaxy_user_group: vgl_galaxy
__galaxy_user_group: vgl_galaxy
galaxy_commit_id: release_22.01
galaxy_force_checkout: true
miniconda_prefix: "{{ galaxy_tool_dependency_dir }}/_conda"
miniconda_version: 4.7.12
miniconda_manage_dependencies: false
galaxy_config:
galaxy:
brand: giraffe
admin: admin@admin.org
database_connection: "postgresql://vgl_galaxy@localhost:5432/galaxy"
file_path: /lustre/fs5/vgl/scratch/vgl_galaxy/galaxy_data/
check_migrate_tools: false
object_store_store_by: uuid
id_secret: "{{ vault_id_secret }}"
uwsgi:
socket: 127.0.0.1:5000
buffer-size: 16384
processes: 1
threads: 4
offload-threads: 2
static-map:
- /static={{ galaxy_server_dir }}/static
- /favicon.ico={{ galaxy_server_dir }}/static/favicon.ico
static-safe: client/galaxy/images
master: true
virtualenv: "{{ galaxy_venv_dir }}"
pythonpath: "{{ galaxy_server_dir }}/lib"
module: galaxy.webapps.galaxy.buildapp:uwsgi_app()
thunder-lock: true
die-on-term: true
hook-master-start:
- unix_signal:2 gracefully_kill_them_all
- unix_signal:15 gracefully_kill_them_all
py-call-osafterfork: true
enable-threads: true
mule:
- lib/galaxy/main.py
- lib/galaxy/main.py
farm: job-handlers:1,2
# systemd
galaxy_manage_systemd: yes
galaxy_systemd_root: false
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