PACKAGER'S README FOR OMERO-5.6.3
Damien Goutte-Gattat <firstname.lastname@example.org>
This file does not come from the OMERO project and the OMERO
developers don't endorse anything of it. Official documentation and
instructions for installing and running OMERO server should be looked
for at <https://docs.openmicroscopy.org/omero/5.6.2/sysadmins/index.html>.
2. SYSTEM USERS AND GROUPS
The OMERO server installed by this SlackBuild is intended to be run
by a dedicated `omero' user. That user will own most of the OMERO
files and must also have a existing, writable HOME directory.
The `doinst.sh' script will automatically create that user if it does
not already exist in `/etc/passwd'. The new account will have a UID
of 270, a HOME directory in `/var/lib/omero' and will belong to the
`omero' group; that group will also be automatically created if
To use another UID/GID or another HOME directory, either edit the
`doinst.sh' script before running the SlackBuild, or create the group
and user yourself before installing the package.
3. INSTALLATION LAYOUT
There are three locations on the filesystem that will be used by the
- the OMERO main directory, `/opt/omero', where the programs and
libraries themselves will be installed;
- the `omero' user's home directory, by default `/var/lib/omero'
(as created by the `doinst.sh' script, see above); it will hold
some temporary files;
- the data repository, where OMERO will store the raw data files,
`/OMERO' by default.
The three locations must be readable and writable by the `omero' user.
The main directory is hardcoded in the SlackBuild and the associated
scripts, but not in OMERO itself; you may change it if you want before
running the SlackBuild.
The `omero' user's home directory can be changed at any time with
usermod(8). Restart OMERO for the change to take effect.
The data repository is defined by the key `omero.data.dir' in the
4. OMERO CONFIGURATION AND CONTROL
There are many parameters controlling OMERO's behavior, but most of
them may be left unmodified for the first run. The only parameters
that must be explicitly set before running OMERO are those defining
the data repository (`omero.data.dir' and `omero.managed.dir') and
the database backend (`omero.db.*').
All parameters may be set by running the `omero config` command under
the `omero` account. For example, to set the directory of the data
$ omero config set omero.data.dir /data/omero
Parameters may also be defined in a `/etc/omero.conf` files, using
the same format as the `omero.properties` file provided with OMERO.
Starting and stoping OMERO is done with the `/etc/rc.d/rc.omero'
control script. Before starting OMERO the first time, run
`/etc/rc.d/rc.omero init'; the script will read the configuration
file `/etc/omero.conf` if it exists and ensure the data repository
and the database backend are ready to use (this includes
automatically creating the PostgreSQL account and database if those
specified in `/etc/omero/omero.properties' does not exist on the
server). This initialization step should be performed each time the
`/etc/omero.conf` is modified.
The Django-based web application OMERO.web is no longer packaged
along with OMERO.server. Use the n/omero-web package to install it.
Make sure Nginx and Django are installed. Add the following line to
the OMERO configuration file /etc/omero.conf:
Then, use the following command to produce a configuration snippet
that can be directly inserted into the configuration of Nginx:
omero web config nginx
Start the web server, the OMERO server itself and the OMERO.web
workers using the rc scripts provided in the corresponding packages.
6. BACKUP AND RESTORE
There are two different items to backup:
- the data directory (/OMERO by default, see 4. above);
- the PostgreSQL database.
The following commands backup everything into /backup:
$ pg_dump -h localhost -U postgres -C omero > /backup/omero.sql
$ rsync --archive --delete --compress --prune-empty-dirs \
To restore, copy the data files back to their locations and reload
the database from the SQL dump.
For general informations about upgrading OMERO, see:
To upgrade OMERO 5.5.x to OMERO-5.6.3:
- Make sure you have Python3, as OMERO-5.6.x no longer supports Python2;
- stop OMERO if it is running;
- backup the SQL database;
- upgrade the package;
- start the upgraded server:
# /etc/rc.d/rc.omero start