Galaxyctl: Galaxy management¶
Galaxyctl is a python script collection used for Galaxy management. In particular it exploits galaxyctl_libs to properly check uWSGI Stats sto correctly retrieve Galaxy and uWSGI workers status.
Moreover the script allow to manage, using the same command, luks volume and onedata spaces, parsing luksctl and onedatctl commands.
Since the script parse supervisorctl or systemd commands, it needs to be run as superuser.
| Moudule | Action | Description |
|---|---|---|
| galaxy | status | Show galaxy status |
| stop | Stop Galaxy. --force check uwsgi master process. If it is still running, after galaxy stop, it is killed. |
|
| start | Start Galaxy. --force force galaxy to start by restarting it. --retry option allow to specify number of tentative retart (default 5). --timeout allow to customize uWSGI stats server wait time. These options are used during galaxy instantiation and you should not use them on production. |
|
| restart | Restart Galaxy. --force force galaxy to start by restarting it. --retry option allow to specify number of tentative retart (default 5). --timeout allow to customize uWSGI stats server wait time. These options are used during galaxy instantiation and you should not use them on production. |
|
| startup | This method is used only to run galaxy for the first time and you shoud not use it in production. --retry option allow to specify number of tentative retart (default 5). --timeout allow to customize uWSGI stats server wait time. |
|
| luks | status | Show LUKS volume status |
| open | LUKSOpen volume | |
| close | LUKSClose volume | |
| onedata | status | Show onedata space status. --userdata allow to check user data space if mounte through oneclient. --refdata allow to check reference data onedata space if mounted through oneclient. |
| mount | Mount onedata space using oneclient. Use --userdata or --refdata to mount user data and reference data volumes. |
|
| umount | Umount onedata space using furermount. |
Galaxyctl basic usage¶
The script requires superuser commands to be used. Its basic commands are:
| Action | Command |
|---|---|
| Start Galaxy | sudo galaxyctl start galaxy |
| Stop Galaxy | sudo galaxyctl stop galaxy |
| Restart Galaxy | sudo galaxyctl restart galaxy |
| Check Galaxy Status | sudo galaxyctl status galaxy |
Logging¶
Logs are stored in /var/log/galaxy/galaxyctl.log file.
Advanced options¶
stop¶
To stop galaxy:
sudo galaxyctl stop galaxy
The script check the uWSGI Stats server to retrieve workers PID and their status. If, after uWSGI stop, workers are still up and running, they are killed, allowing Galaxy to correctly start next time.
The --force options allow to kill uwsgi master process if it is still alive after galaxy stop (in case of uwsgi FATAL error or ABNORMAL TERMINATION). Please check galaxy logs before run --force option.
start¶
To start Galaxy:
sudo galaxyctl start galaxy
Once Galaxy started, galaxyctl waits and check the uWSGI Stats server. Since it is the last software loaded, this ensure that Galaxy has correctly started. The script also check that at least 1 uWSGI worker has correctly started and it is accepting requests.
If no workers are available you have to restart Galaxy.
Galaxyctl is able to automatically restart galaxy if the option --force is specified, restarting it until the workers are correctly loaded
The number of retries is set, by default, to 5. It can be customized using --retry option, e.g. --retry 10.
These options were not designed for production, but are used only during VMs instantiation phase to ensure Galaxy can correctly start.
restart¶
To restart Galaxy:
sudo galaxyctl restart galaxy
The options --force, --timeout and --retry are available for restart command too.
Galaxy first start¶
Galaxy takes longer to start the first time. Since the uWSGI stats server is the last software component started, the script waits it ensure that Galaxy has correctly started. Then uWSGI workers are checked to ensure Galaxy is acceptin requests. If not, uWSGI is restarted.
Currently, before rise an error, the script try to restart galaxy 5 times, while the waiting time is set to 600 seconds.
The command used in /usr/local/bin/galaxy-startup script, is
galaxyctl startup galaxy -c /home/galaxy/galaxy/galaxy.ini -t 600
LUKS module¶
By parsing luksctl script and using galaxyctl_libs, galaxyctl is able to manage LUKS volumes
| Action | Command |
|---|---|
| Open LUKS volume | sudo galaxyctl open luks |
| Close LUKS volume | sudo galaxyctl close luks |
| Check LUKS volume | sudo galaxyctl status luks |
In particular to unlock you LUKS volume:
sudo galaxyctl open luks
Then you will be asket to insert your LUKS passphrase. For instance:
(.venv) [galaxy@galaxy-indigo-test ~]$ sudo galaxyctl open luks
Enter passphrase for /dev/disk/by-uuid/42aaf979-6351-44e9-97ee-19e7f8c5e9f6:
Onedata module¶
By parsing onedatactl script and using galaxyctl_libs, galaxyctl is able to manage onedata user data and reference data spaces.
| Data | Action | Command |
|---|---|---|
| User data | mount | sudo galaxyctl mount onedata –userdata |
| umount | sudo galaxyctl umount onedata –userdata | |
| status | sudo galaxyctl status onedata –userdata | |
| Refarence data | mount | sudo galaxyctl mount onedata –refdata |
| umount | sudo galaxyctl umount onedata –userdata | |
| status | sudo galaxyctl status onedata –refdata |
The options --userdata and --refdata are mutually exclusive.
Configuration files¶
Supervisord and systemd/upstart are supported to start/stop/restart/status Galaxy.
The init system can be set using the variables init_system: two values are, currently, allowed: supervisord and init
| init_system | Explanation |
|---|---|
| supervisord | Supervisord is current default, it is mandatory for docker container, since there’s no systemd on docker images. |
| init | CentOS 7 and Ubuntu 16.04 use systemd, while Ubuntu 14.04 is using upstart. |
Through galaxyctl_libs.DetectGalaxyCommands method the script automatically retrieve the right command to be used and it is compatible with both CentOS 7 and Ubuntu (14.04 and 16.04).
If Supervisord is used to manage Galaxy (which is our default choice), configuration files have to be specified using the variable supervisord_config_file
On CentOS:
supervisord_conf_file = '/etc/supervisord.conf'
while on Ubuntu:
supervisord_conf_file = '/etc/supervisor/supervisord.conf'
Galaxyctl needs galaxy.ini to retrieve uWSGI stats server information, through the variable:
galaxy_config_file = '/home/galaxy/galaxy/config/galaxy.ini'
For LUKS volume configuration, the script reads our custom luks-cryptdev.ini file (stored in /etc/galaxy/ and needs luksctl script path (usually stored in /usr/local/bin) to load methods
luks_config_file = '/etc/galaxy/luks-cryptdev.ini'
luksctl_path = '/usr/local/bin'
Finally, for onedata spaces management, onedatactl.ini file (stored in /etc/galaxy) and onedatactl path (usually /usr/local/bin) are needed:
onedatactl_config_file = '/etc/galaxy/onedatactl.ini'
onedatactl_path = '/usr/local/bin'