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ARTbio / GalaxyKickStart

Ansible playbooks for Galaxy Server deployment
GNU General Public License v3.0
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new rsync error with ansible metavisitor ? #154

Closed drosofff closed 8 years ago

drosofff commented 8 years ago

In short, I have this:

TASK [galaxy.movedata : Copy galaxy data/config directories to permanent directories] ***
changed: [192.54.201.116] => (item={u'owner': u'galaxy', u'path': u'/home/galaxy/tool_dependencies'})
failed: [192.54.201.116] => (item={u'owner': u'galaxy', u'path': u'/home/galaxy/galaxy/../shed_tools'}) => {"changed": true, "cmd": "rsync --exclude \".original\" -a /home/galaxy/galaxy/../shed_tools/ /root/mydisk//home/galaxy/galaxy/../shed_tools", "delta": "0:00:00.123741", "end": "2016-05-09 22:07:59.243474", "failed": true, "item": {"owner": "galaxy", "path": "/home/galaxy/galaxy/../shed_tools"}, "rc": 23, "start": "2016-05-09 22:07:59.119733", "stderr": "rsync: change_dir \"/home/galaxy/galaxy/../shed_tools\" failed: No such file or directory (2)\nrsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1183) [sender=3.1.0]", "stdout": "", "stdout_lines": [], "warnings": ["Consider using synchronize module rather than running rsync"]}
 [WARNING]: Consider using synchronize module rather than running rsync

and in extenso, this

imac-chris:ansible-artimed aligre$ ansible-playbook --inventory-file=hosts galaxy.yml
[DEPRECATION WARNING]: Instead of sudo/sudo_user, use become/become_user and make sure become_method is 'sudo' (default). This feature will be removed in a future release. Deprecation warnings can be disabled by setting deprecation_warnings=False in 
ansible.cfg.

PLAY ***************************************************************************

TASK [setup] *******************************************************************
The authenticity of host '192.54.201.116 (192.54.201.116)' can't be established.
ECDSA key fingerprint is SHA256:39WcETOtVJ3ELtxCTJd0AJ09iEcZr8nRz46B5v3B4DY.
Are you sure you want to continue connecting (yes/no)? yes
ok: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-os : include] *********************************
included: /Users/aligre/ansible-artimed/roles/galaxyprojectdotorg.galaxy-os/tasks/system_users.yml for 192.54.201.116

TASK [galaxyprojectdotorg.galaxy-os : Add system groups] ***********************
changed: [192.54.201.116] => (item={u'gid': 1450, u'name': u'galaxy'})
changed: [192.54.201.116] => (item={u'gid': 1550, u'name': u'postgres'})

TASK [galaxyprojectdotorg.galaxy-os : Add shadow groups] ***********************
ok: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-os : Add postgres user] ***********************
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-os : Adjust postgresql permissions] ***********
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-os : Add galaxy user] *************************
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-os : Add nobody user to shadow group] *********
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-os : include] *********************************
included: /Users/aligre/ansible-artimed/roles/galaxyprojectdotorg.galaxy-os/tasks/packages.yml for 192.54.201.116

TASK [galaxyprojectdotorg.galaxy-os : Add custom Galaxy PPA (used for nginx package)] ***
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-os : Add custom Galaxy PPA (used for nginx package)] ***
skipping: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-os : Add Docker repository key] ***************
ok: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-os : Add Docker repository] *******************
ok: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-os : Update APT cache] ************************
ok: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-os : Install required system packages] ********
changed: [192.54.201.116] => (item=[u'ant', u'cmake', u'curl', u'g++', u'gcc', u'gfortran', u'git-core', u'libffi-dev', u'liblapack-dev', u'libncurses5-dev', u'libopenblas-dev', u'libpam0g-dev', u'libpq-dev', u'libsparsehash-dev', u'make', u'mercurial', u'nginx-extras', u'openssh-server', u'patch', u'pkg-config', u'postgresql', u'postgresql', u'postgresql-client', u'python-boto', u'python-dev', u'python-prettytable', u'python-psycopg2', u'python-virtualenv', u'python-pip', u'rsync', u'slurm-drmaa-dev', u'supervisor', u'swig', u'sysstat', u'unzip', u'wget', u'zlib1g-dev'])

TASK [galaxyprojectdotorg.galaxy-os : Install packages for system maintenance] *
skipping: [192.54.201.116] => (item=[]) 

TASK [galaxyprojectdotorg.galaxy-os : Install required system packages - release_specific] ***
changed: [192.54.201.116] => (item=[u'postgresql-plpython-9.3', u'postgresql-server-dev-9.3'])

TASK [galaxyprojectdotorg.galaxy-os : Install required system packages - 15.10] 
skipping: [192.54.201.116] => (item=[]) 

TASK [galaxyprojectdotorg.galaxy-os : include] *********************************
included: /Users/aligre/ansible-artimed/roles/galaxyprojectdotorg.galaxy-os/tasks/docker.yml for 192.54.201.116

TASK [galaxyprojectdotorg.galaxy-os : Install Docker package] ******************
ok: [192.54.201.116] => (item=[u'docker-engine'])

TASK [galaxyprojectdotorg.galaxy-os : Install apparmor] ************************
skipping: [192.54.201.116] => (item=[]) 

TASK [galaxyprojectdotorg.galaxy-os : Allow galaxy user to run docker with sudo] ***
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-os : Add Galaxy user to docker group - allowing sudoless docker usage] ***
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-os : Set DOCKER_OPTS] *************************
changed: [192.54.201.116]

TASK [ensure_postgresql_up : service] ******************************************
ok: [192.54.201.116]

TASK [ensure_postgresql_up : supervisorctl] ************************************
fatal: [192.54.201.116]: FAILED! => {"changed": false, "failed": true, "msg": "ERROR: no such process/group: postgresql\n", "name": "postgresql", "state": "present"}
...ignoring

TASK [ensure_postgresql_up : supervisorctl] ************************************
skipping: [192.54.201.116]

TASK [ensure_postgresql_up : service] ******************************************
ok: [192.54.201.116]

TASK [ensure_postgresql_up : command] ******************************************
changed: [192.54.201.116]

TASK [ensure_postgresql_up : discover location of pg_data] *********************
ok: [192.54.201.116]

TASK [ensure_postgresql_up : discover postgres version] ************************
ok: [192.54.201.116]

TASK [ensure_postgresql_up : set_fact] *****************************************
ok: [192.54.201.116]

TASK [natefoo.postgresql_objects : Revoke extra privileges] ********************
[DEPRECATION WARNING]: Using bare variables is deprecated. Update your playbooks so that the environment value uses the full variable syntax ('{{postgresql_objects_privileges}}'). This feature will be removed in a future release. Deprecation warnings can
 be disabled by setting deprecation_warnings=False in ansible.cfg.

TASK [natefoo.postgresql_objects : Drop databases] *****************************
[DEPRECATION WARNING]: Using bare variables is deprecated. Update your playbooks so that the environment value uses the full variable syntax ('{{postgresql_objects_databases}}'). This feature will be removed in a future release. Deprecation warnings can 
be disabled by setting deprecation_warnings=False in ansible.cfg.
skipping: [192.54.201.116] => (item={u'owner': u'galaxy', u'name': u'galaxy'}) 

TASK [natefoo.postgresql_objects : Create and drop users] **********************
[DEPRECATION WARNING]: Using bare variables is deprecated. Update your playbooks so that the environment value uses the full variable syntax ('{{postgresql_objects_users}}'). This feature will be removed in a future release. Deprecation warnings can be 
disabled by setting deprecation_warnings=False in ansible.cfg.
changed: [192.54.201.116] => (item={u'password': u'galaxy', u'name': u'galaxy'})

TASK [natefoo.postgresql_objects : Create groups] ******************************
[DEPRECATION WARNING]: Using bare variables is deprecated. Update your playbooks so that the environment value uses the full variable syntax ('{{postgresql_objects_groups}}'). This feature will be removed in a future release. Deprecation warnings can be 
disabled by setting deprecation_warnings=False in ansible.cfg.

TASK [natefoo.postgresql_objects : Add or remove users from groups] ************
[DEPRECATION WARNING]: Using bare variables is deprecated. Update your playbooks so that the environment value uses the full variable syntax ('{{postgresql_objects_groups}}'). This feature will be removed in a future release. Deprecation warnings can be 
disabled by setting deprecation_warnings=False in ansible.cfg.

TASK [natefoo.postgresql_objects : Drop groups] ********************************
[DEPRECATION WARNING]: Using bare variables is deprecated. Update your playbooks so that the environment value uses the full variable syntax ('{{postgresql_objects_groups}}'). This feature will be removed in a future release. Deprecation warnings can be 
disabled by setting deprecation_warnings=False in ansible.cfg.

TASK [natefoo.postgresql_objects : Create databases] ***************************
[DEPRECATION WARNING]: Using bare variables is deprecated. Update your playbooks so that the environment value uses the full variable syntax ('{{postgresql_objects_databases}}'). This feature will be removed in a future release. Deprecation warnings can 
be disabled by setting deprecation_warnings=False in ansible.cfg.
changed: [192.54.201.116] => (item={u'owner': u'galaxy', u'name': u'galaxy'})

TASK [natefoo.postgresql_objects : Grant user database privileges] *************
[DEPRECATION WARNING]: Using bare variables is deprecated. Update your playbooks so that the environment value uses the full variable syntax ('{{postgresql_objects_users}}'). This feature will be removed in a future release. Deprecation warnings can be 
disabled by setting deprecation_warnings=False in ansible.cfg.
skipping: [192.54.201.116] => (item={u'password': u'galaxy', u'name': u'galaxy'}) 

TASK [natefoo.postgresql_objects : Grant extra privileges] *********************
[DEPRECATION WARNING]: Using bare variables is deprecated. Update your playbooks so that the environment value uses the full variable syntax ('{{postgresql_objects_privileges}}'). This feature will be removed in a future release. Deprecation warnings can
 be disabled by setting deprecation_warnings=False in ansible.cfg.

TASK [galaxyprojectdotorg.galaxy : include] ************************************
included: /Users/aligre/ansible-artimed/roles/galaxyprojectdotorg.galaxy/tasks/clone.yml for 192.54.201.116

TASK [galaxyprojectdotorg.galaxy : Check for Galaxy] ***************************
ok: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy : Get current Galaxy changeset (hg)] **********
skipping: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy : Get current Galaxy commit id (git)] *********
skipping: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy : Report current Galaxy changeset] ************
skipping: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy : Update Galaxy to correct changeset (hg)] ****
skipping: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy : Update Galaxy to correct changeset (git)] ***
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy : include] ************************************
included: /Users/aligre/ansible-artimed/roles/galaxyprojectdotorg.galaxy/tasks/virtualenv.yml for 192.54.201.116

TASK [galaxyprojectdotorg.galaxy : Create Galaxy virtualenv] *******************
ok: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy : Remove orphaned .pyc files and compile bytecode] ***
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy : include] ************************************
skipping: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy : include] ************************************
included: /Users/aligre/ansible-artimed/roles/galaxyprojectdotorg.galaxy/tasks/static_setup.yml for 192.54.201.116

TASK [galaxyprojectdotorg.galaxy : Create Galaxy config dir] *******************
ok: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy : Install additional Galaxy config files (static)] ***
[DEPRECATION WARNING]: Using bare variables is deprecated. Update your playbooks so that the environment value uses the full variable syntax ('{{galaxy_config_files}}'). This feature will be removed in a future release. Deprecation warnings can be 
disabled by setting deprecation_warnings=False in ansible.cfg.

TASK [galaxyprojectdotorg.galaxy : Install additional Galaxy config files (template)] ***
[DEPRECATION WARNING]: Using bare variables is deprecated. Update your playbooks so that the environment value uses the full variable syntax ('{{galaxy_config_templates}}'). This feature will be removed in a future release. Deprecation warnings can be 
disabled by setting deprecation_warnings=False in ansible.cfg.

TASK [galaxyprojectdotorg.galaxy : Create Galaxy configuration file] ***********
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy : include] ************************************
included: /Users/aligre/ansible-artimed/roles/galaxyprojectdotorg.galaxy/tasks/dependencies.yml for 192.54.201.116

TASK [galaxyprojectdotorg.galaxy : Check if Galaxy uses eggs or wheels] ********
ok: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy : Fetch Galaxy eggs] **************************
skipping: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy : Install Galaxy pip] *************************
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy : Create binary-compatibility.cfg if necessary] ***
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy : Install Galaxy base dependencies] ***********
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy : Collect Galaxy conditional dependency requirement strings] ***
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy : Install Galaxy conditional dependencies] ****
[DEPRECATION WARNING]: Using bare variables is deprecated. Update your playbooks so that the environment value uses the full variable syntax ('{{conditional_dependencies.stdout_lines}}'). This feature will be removed in a future release. Deprecation 
warnings can be disabled by setting deprecation_warnings=False in ansible.cfg.
changed: [192.54.201.116] => (item=psycopg2==2.6.1)

TASK [galaxyprojectdotorg.galaxy : include] ************************************
included: /Users/aligre/ansible-artimed/roles/galaxyprojectdotorg.galaxy/tasks/mutable_setup.yml for 192.54.201.116

TASK [galaxyprojectdotorg.galaxy : Create mutable configuration file directory] 
ok: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy : Instantiate mutable configuration files] ****
[DEPRECATION WARNING]: Using bare variables is deprecated. Update your playbooks so that the environment value uses the full variable syntax ('{{galaxy_mutable_configs}}'). This feature will be removed in a future release. Deprecation warnings can be 
disabled by setting deprecation_warnings=False in ansible.cfg.
changed: [192.54.201.116] => (item={u'dest': u'/home/galaxy/galaxy/config/shed_tool_conf.xml', u'src': u'/home/galaxy/galaxy/config/shed_tool_conf.xml.sample'})
changed: [192.54.201.116] => (item={u'dest': u'/home/galaxy/galaxy/config/migrated_tools_conf.xml', u'src': u'/home/galaxy/galaxy/config/migrated_tools_conf.xml.sample'})
changed: [192.54.201.116] => (item={u'dest': u'/home/galaxy/galaxy/config/shed_data_manager_conf.xml', u'src': u'/home/galaxy/galaxy/config/shed_data_manager_conf.xml.sample'})
changed: [192.54.201.116] => (item={u'dest': u'/home/galaxy/galaxy/config/shed_tool_data_table_conf.xml', u'src': u'/home/galaxy/galaxy/config/shed_tool_data_table_conf.xml.sample'})

TASK [galaxyprojectdotorg.galaxy : include] ************************************
included: /Users/aligre/ansible-artimed/roles/galaxyprojectdotorg.galaxy/tasks/database.yml for 192.54.201.116

TASK [galaxyprojectdotorg.galaxy : Get current Galaxy DB version] **************
ok: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy : Get maximum Galaxy DB version] **************
ok: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy : Create Galaxy DB] ***************************
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy : Upgrade Galaxy DB] **************************
skipping: [192.54.201.116]

TASK [set_supervisor_env_vars : Install supervisor] ****************************
ok: [192.54.201.116]

TASK [set_supervisor_env_vars : Add supervisor ENV vars] ***********************
changed: [192.54.201.116] => (item=export IP_ADDRESS=`curl --silent icanhazip.com`)
changed: [192.54.201.116] => (item=export MASQUERADE_ADDRESS=$IP_ADDRESS)
changed: [192.54.201.116] => (item=export NATIVE_SPEC="--ntasks=`/usr/bin/nproc` --share")
changed: [192.54.201.116] => (item=export NGINX_GALAXY_LOCATION="")
changed: [192.54.201.116] => (item=export GALAXY_CONFIG_FTP_UPLOAD_SITE="ftp://$IP_ADDRESS")
changed: [192.54.201.116] => (item=export GALAXY_CONFIG_NGINX_X_ACCEL_REDIRECT_BASE="$NGINX_GALAXY_LOCATION/_x_accel_redirect")
changed: [192.54.201.116] => (item=export GALAXY_CONFIG_NGINX_X_ARCHIVE_FILES_BASE="$NGINX_GALAXY_LOCATION/_x_accel_redirect")
changed: [192.54.201.116] => (item=export GALAXY_CONFIG_NGINX_UPLOAD_PATH="$NGINX_GALAXY_LOCATION/_upload")

TASK [set_supervisor_env_vars : restart supervisor] ****************************
changed: [192.54.201.116]

TASK [copy_additional_files : Copy additional files] ***************************
changed: [192.54.201.116] => (item={u'dest': u'/home/galaxy/galaxy/static/', u'src': u'extra-files/metavisitor/welcome.html'})
changed: [192.54.201.116] => (item={u'dest': u'/home/galaxy/galaxy/static/images/', u'src': u'extra-files/metavisitor/metavisitor_logo.png'})

TASK [galaxyprojectdotorg.galaxy-extras : include] *****************************
included: /Users/aligre/ansible-artimed/roles/galaxyprojectdotorg.galaxy-extras/tasks/galaxy_root.yml for 192.54.201.116

TASK [galaxyprojectdotorg.galaxy-extras : Run common_startup.sh to create welcome.html from sample] ***
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : Install watchdog for galaxy] *********
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : include] *****************************
included: /Users/aligre/ansible-artimed/roles/galaxyprojectdotorg.galaxy-extras/tasks/galaxy_metrics.yml for 192.54.201.116

TASK [galaxyprojectdotorg.galaxy-extras : Setup job metrics] *******************
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : include] *****************************
included: /Users/aligre/ansible-artimed/roles/galaxyprojectdotorg.galaxy-extras/tasks/uwsgi.yml for 192.54.201.116

TASK [galaxyprojectdotorg.galaxy-extras : Install uwsgi for galaxy] ************
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : include] *****************************
included: /Users/aligre/ansible-artimed/roles/galaxyprojectdotorg.galaxy-extras/tasks/nginx.yml for 192.54.201.116

TASK [galaxyprojectdotorg.galaxy-extras : Create nginx configuration file] *****
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : Create nginx upload_store dir] *******
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : Create nginx uwsgi configuration] ****
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : Create nginx Galaxy web configuration] ***
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : Create nginx IDE configuration] ******
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : Add htpasswd file.] ******************
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : include] *****************************
included: /Users/aligre/ansible-artimed/roles/galaxyprojectdotorg.galaxy-extras/tasks/proftpd.yml for 192.54.201.116

TASK [galaxyprojectdotorg.galaxy-extras : Install proftpd related system packages] ***
changed: [192.54.201.116] => (item=[u'proftpd', u'proftpd-mod-pgsql'])

TASK [galaxyprojectdotorg.galaxy-extras : Create Galaxy configuration file] ****
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : Load Proftpd modules] ****************
changed: [192.54.201.116] => (item=LoadModule mod_sql.c)
changed: [192.54.201.116] => (item=LoadModule mod_sql_passwd.c)
changed: [192.54.201.116] => (item=LoadModule mod_sql_postgres.c)

TASK [galaxyprojectdotorg.galaxy-extras : include] *****************************
included: /Users/aligre/ansible-artimed/roles/galaxyprojectdotorg.galaxy-extras/tasks/slurm.yml for 192.54.201.116

TASK [galaxyprojectdotorg.galaxy-extras : Install pip] *************************
ok: [192.54.201.116] => (item=[u'python-pip'])

TASK [galaxyprojectdotorg.galaxy-extras : Install SLURM system packages] *******
changed: [192.54.201.116] => (item=[u'munge', u'slurm-llnl', u'slurm-drmaa-dev', u'python-psutil'])

TASK [galaxyprojectdotorg.galaxy-extras : Install SLURM system packages] *******
changed: [192.54.201.116] => (item=[u'slurm-llnl-torque'])

TASK [galaxyprojectdotorg.galaxy-extras : Install SLURM system packages] *******
skipping: [192.54.201.116] => (item=[]) 

TASK [galaxyprojectdotorg.galaxy-extras : Create Munge Key] ********************
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : Setup Munge permissions and folder] **
changed: [192.54.201.116] => (item=/var/run/munge)
changed: [192.54.201.116] => (item=/var/lib/munge)
changed: [192.54.201.116] => (item=/var/log/munge)
ok: [192.54.201.116] => (item=/var/run/munge)
changed: [192.54.201.116] => (item=/etc/munge)

TASK [galaxyprojectdotorg.galaxy-extras : Setup tmp area for slurm.] ***********
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : Create slurm configuration file] *****
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : Check if Galaxy uses eggs or wheels] *
ok: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : Fetch DRMAA egg for Galaxy] **********
skipping: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : Fetch DRMAA wheel for Galaxy] ********
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : Install Galaxy job conf] *************
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : include] *****************************
skipping: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : include] *****************************
included: /Users/aligre/ansible-artimed/roles/galaxyprojectdotorg.galaxy-extras/tasks/supervisor.yml for 192.54.201.116

TASK [galaxyprojectdotorg.galaxy-extras : Install web related system packages] *
changed: [192.54.201.116] => (item=[u'uwsgi', u'uwsgi-plugin-python', u'supervisor'])

TASK [galaxyprojectdotorg.galaxy-extras : Create Galaxy configuration file] ****
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : Stop supervisor] *********************
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : Stop and remove uwsgi.] **************
changed: [192.54.201.116] => (item=uwsgi)

TASK [galaxyprojectdotorg.galaxy-extras : Stop and remove munge.] **************
changed: [192.54.201.116] => (item=munge)

TASK [galaxyprojectdotorg.galaxy-extras : Stop and remove slurm.] **************
changed: [192.54.201.116] => (item=slurm-llnl)

TASK [galaxyprojectdotorg.galaxy-extras : Stop and remove slurm.] **************
skipping: [192.54.201.116] => (item=slurmd) 
skipping: [192.54.201.116] => (item=slurmctld) 

TASK [galaxyprojectdotorg.galaxy-extras : Stop and remove postgresql.] *********
changed: [192.54.201.116] => (item=postgresql)

TASK [galaxyprojectdotorg.galaxy-extras : Stop and remove proftpd.] ************
changed: [192.54.201.116] => (item=proftpd)

TASK [galaxyprojectdotorg.galaxy-extras : Stop and remove nginx.] **************
changed: [192.54.201.116] => (item=nginx)

TASK [galaxyprojectdotorg.galaxy-extras : Start supervisor] ********************
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : include] *****************************
skipping: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : include] *****************************
included: /Users/aligre/ansible-artimed/roles/galaxyprojectdotorg.galaxy-extras/tasks/galaxy_scripts.yml for 192.54.201.116

TASK [galaxyprojectdotorg.galaxy-extras : Install repository intallation script.] ***
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : Install galaxy user creation script.] 
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : Install export user files script.] ***
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : include] *****************************
included: /Users/aligre/ansible-artimed/roles/galaxyprojectdotorg.galaxy-extras/tasks/startup.yml for 192.54.201.116

TASK [galaxyprojectdotorg.galaxy-extras : Install cgroupfs_mount.sh for startup script.] ***
changed: [192.54.201.116]

TASK [galaxyprojectdotorg.galaxy-extras : Install startup script used to configure container.] ***
changed: [192.54.201.116]

TASK [ensure_postgresql_up : service] ******************************************
ok: [192.54.201.116]

TASK [ensure_postgresql_up : supervisorctl] ************************************
ok: [192.54.201.116]

TASK [ensure_postgresql_up : supervisorctl] ************************************
ok: [192.54.201.116]

TASK [ensure_postgresql_up : service] ******************************************
skipping: [192.54.201.116]

TASK [ensure_postgresql_up : command] ******************************************
changed: [192.54.201.116]

TASK [ensure_postgresql_up : discover location of pg_data] *********************
ok: [192.54.201.116]

TASK [ensure_postgresql_up : discover postgres version] ************************
ok: [192.54.201.116]

TASK [ensure_postgresql_up : set_fact] *****************************************
ok: [192.54.201.116]

TASK [artimed_extras : include] ************************************************
included: /Users/aligre/ansible-artimed/roles/artimed_extras/tasks/galaxy_admin.yml for 192.54.201.116

TASK [artimed_extras : Create/invoke script virtualenv for create galaxy admin] 
ok: [192.54.201.116] => (item=pyyaml)
ok: [192.54.201.116] => (item=bioblend)

TASK [artimed_extras : Create Galaxy admin user] *******************************
changed: [192.54.201.116]

TASK [artimed_extras : include] ************************************************
included: /Users/aligre/ansible-artimed/roles/artimed_extras/tasks/extras.yml for 192.54.201.116

TASK [artimed_extras : Create proftpd dir] *************************************
changed: [192.54.201.116]

TASK [artimed_extras : Manage template for proftpd] ****************************
changed: [192.54.201.116] => (item={u'dest': u'/etc/proftpd/proftpd.conf', u'src': u'proftpd.conf.j2'})

TASK [artimed_extras : Create tool dependency dir] *****************************
changed: [192.54.201.116]

TASK [artimed_extras : Restart/start supervisor tasks] *************************
changed: [192.54.201.116] => (item={u'state': u'restarted', u'name': u'proftpd'})
ok: [192.54.201.116] => (item={u'state': u'started', u'name': u'munge'})
ok: [192.54.201.116] => (item={u'state': u'started', u'name': u'nginx'})

TASK [artimed_extras : include] ************************************************
skipping: [192.54.201.116]

TASK [artimed_extras : include] ************************************************
skipping: [192.54.201.116]

TASK [galaxy.movedata : Check for persistent directory] ************************
ok: [192.54.201.116]

TASK [galaxy.movedata : Check for persistent data] *****************************
ok: [192.54.201.116]

TASK [galaxy.movedata : Check if galaxy config dir should be imported (no .original file)] ***
ok: [192.54.201.116]

TASK [galaxy.movedata : include] ***********************************************
skipping: [192.54.201.116]

TASK [galaxy.movedata : include] ***********************************************
included: /Users/aligre/ansible-artimed/roles/galaxy.movedata/tasks/export.yml for 192.54.201.116

TASK [galaxy.movedata : Stop supervisor tasks to copy data/config directories to the permanent directories] ***
changed: [192.54.201.116] => (item=galaxy:)
changed: [192.54.201.116] => (item=proftpd)
changed: [192.54.201.116] => (item=postgresql)

TASK [galaxy.movedata : Create persistent directory paths] *********************
changed: [192.54.201.116] => (item={u'owner': u'galaxy', u'path': u'/home/galaxy/tool_dependencies'})
changed: [192.54.201.116] => (item={u'owner': u'galaxy', u'path': u'/home/galaxy/galaxy/../shed_tools'})
changed: [192.54.201.116] => (item={u'owner': u'galaxy', u'path': u'/home/galaxy/galaxy/tool-data'})
changed: [192.54.201.116] => (item={u'owner': u'galaxy', u'path': u'/home/galaxy/galaxy/config'})
changed: [192.54.201.116] => (item={u'owner': u'galaxy', u'path': u'/home/galaxy/galaxy/database'})
changed: [192.54.201.116] => (item={u'owner': u'postgres', u'path': u'/var/lib/postgresql/9.3/main'})

TASK [galaxy.movedata : Copy galaxy data/config directories to permanent directories] ***
changed: [192.54.201.116] => (item={u'owner': u'galaxy', u'path': u'/home/galaxy/tool_dependencies'})
failed: [192.54.201.116] => (item={u'owner': u'galaxy', u'path': u'/home/galaxy/galaxy/../shed_tools'}) => {"changed": true, "cmd": "rsync --exclude \".original\" -a /home/galaxy/galaxy/../shed_tools/ /root/mydisk//home/galaxy/galaxy/../shed_tools", "delta": "0:00:00.123741", "end": "2016-05-09 22:07:59.243474", "failed": true, "item": {"owner": "galaxy", "path": "/home/galaxy/galaxy/../shed_tools"}, "rc": 23, "start": "2016-05-09 22:07:59.119733", "stderr": "rsync: change_dir \"/home/galaxy/galaxy/../shed_tools\" failed: No such file or directory (2)\nrsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1183) [sender=3.1.0]", "stdout": "", "stdout_lines": [], "warnings": ["Consider using synchronize module rather than running rsync"]}
 [WARNING]: Consider using synchronize module rather than running rsync

changed: [192.54.201.116] => (item={u'owner': u'galaxy', u'path': u'/home/galaxy/galaxy/tool-data'})
changed: [192.54.201.116] => (item={u'owner': u'galaxy', u'path': u'/home/galaxy/galaxy/config'})
changed: [192.54.201.116] => (item={u'owner': u'galaxy', u'path': u'/home/galaxy/galaxy/database'})
changed: [192.54.201.116] => (item={u'owner': u'postgres', u'path': u'/var/lib/postgresql/9.3/main'})

RUNNING HANDLER [galaxyprojectdotorg.galaxy : restart galaxy] ******************

RUNNING HANDLER [galaxyprojectdotorg.galaxy : email administrator with changeset id] ***
    to retry, use: --limit @galaxy.retry

PLAY RECAP *********************************************************************
192.54.201.116             : ok=124  changed=71   unreachable=0    failed=1
mvdbeek commented 8 years ago

Well, 

"rsync: change_dir \"/home/galaxy/galaxy/../shed_tools\" failed: No such file or directory

Do you have that directory? (/home/galaxy/shed_tools)

drosofff commented 8 years ago

Well, it an ansible install from scratch, new vinstance, new vdisk.

Christophe Antoniewski

ARTbio http://artbio.fr/ - Tel +33 1 44 27 70 05 Drosophila Genetics & Epigenetics http://drosophile.org/ - Tel +33 1 44 2 _7 34 39_Mobile +33 6 68 60 51 50 https://twitter.com/ARTbio_IBPS https://twitter.com/drosofff

2016-05-10 8:40 GMT+02:00 Marius van den Beek notifications@github.com:

Well,

"rsync: change_dir \"/home/galaxy/galaxy/../shed_tools\" failed: No such file or directory

Do you have that directory? (/home/galaxy/shed_tools)

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/ARTbio/ansible-artimed/issues/154#issuecomment-218071647

drosofff commented 8 years ago

I have indeed this:

drwxr-xr-x 5 galaxy galaxy 4096 May  9 22:07 galaxy/
drwxr-xr-x 2 galaxy galaxy 4096 May  9 22:07 shed_tools/
drwxr-xr-x 2 galaxy galaxy 4096 May  9 22:07 tool_dependencies/
root@vm0085:~/mydisk/home/galaxy# pwd
/root/mydisk/home/galaxy

and no /home/galaxy/shed_tools, indeed

-rw-r--r--  1 galaxy users   220 Apr  9  2014 .bash_logout
-rw-r--r--  1 galaxy users  3637 Apr  9  2014 .bashrc
drwx------  3 galaxy users  4096 May  9 22:00 .cache/
drwxr-xr-x  3 galaxy users  4096 May  9 22:00 .distlib/
drwxr-xr-x 23 galaxy users  4096 May  9 22:07 galaxy/
-rw-r--r--  1 galaxy users   675 Apr  9  2014 .profile
drwxr-xr-x  2 galaxy galaxy 4096 May  9 22:07 tool_dependencies/
root@vm0085:/home/galaxy# pwd
/home/galaxy
drosofff commented 8 years ago

It's installing properly now. 👍