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Damien Goutte-Gattat 8fc5164a3f
n/omero: Updated for OMERO.web.
10 years ago
.. n/omero: Upgraded to omero-4.4.6. 10 years ago
README n/omero: Updated for OMERO.web. 10 years ago n/omero: Moved from ap/omero. 12 years ago
omero.SlackBuild n/omero: Updated for OMERO.web. 10 years ago n/omero: Moved from ap/omero. 12 years ago
rc.omero n/omero: Updated for OMERO.web. 10 years ago
slack-desc n/omero: Moved from ap/omero. 12 years ago


                 PACKAGER'S README FOR OMERO-4.4.6

Damien Goutte-Gattat <>


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 <>.


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 `' 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
`' script before running the SlackBuild, or create the group
and user yourself before installing the package.


There are four 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 configuration directory, `/etc/omero', will store all
the configuration files; they should normally be in OMERO's main
directory, but I prefer to have them in `/etc', so I symlink
`/opt/omero/etc' to `/etc/omero' to allow OMERO to find them;

- the `omero' user's home directory, by default `/var/lib/omero'
(as created by the `' script, see above); it will hold
some temporary files and the current runtime configuration of
OMERO, if different from the default built-in configuration;

- the data repository, where OMERO will store the raw data files,
`/OMERO' by default.

The four locations must be readable by the `omero' user; the main
directory, the `omero' user's home directory, and the data repository
must be writable by that user.

The main and configuration directories are hardcoded in the
SlackBuild and the associated scripts, but not in OMERO itself; you
may change them 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 `' in the
main configuration file `/etc/omero/'.


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 (`') and the database backend
(`omero.db.*'), in `/etc/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
files 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/' does not exist on the server). This
initialization step should be performed each time a configuration
file is modified.

5. OMERO.web

The Django-based web application OMERO.web is not enabled by default,
as it requires some configuration.

Add the following lines to the OMERO configuration file


Then, edit the control script /etc/rc.d/rc.omero to automatically
start and start the FCGI workers alongside the OMERO server itself:


The Django-based web application OMERO.web is needed at least to
create OMERO users. By default this application is not enabled. Edit
the control script /etc/rc.d/rc.omero to automatically start and stop
the application alongside the OMERO server itself:


Then, you need to install and configure the Apache HTTP server to
actually serve the application.

NOTE: Do *not* follow the official OMERO documentation from this
point, as it does not support running OMERO.web with Apache 2.4 and
the mod_proxy_fcgi module. In particular, the configuration lines
produced by the following command:

omero web config apache

is not suitable for Apache 2.4.

Instead, add the following stanza to your Apache configuration:

RewriteEngine On
RewriteRule ^/?$ /omero/ [R]

ProxyPass /webclient fcgi://localhost:4080
ProxyPass /webadmin fcgi://localhost:4080

Alias /static /opt/omero/lib/python/omeroweb/static

<Directory "/opt/omero/lib/python/omeroweb/static">
Options -Indexes +FollowSymLinks
Require all granted

(Make sure the mod_rewrite, mod_proxy and mod_proxy_fcgi modules are
loaded. This is normally done in the default httpd configuration file
provided by Slackware.)

Start the web server. OMERO.web should now be reachable at
<http://<hostname>/webclient> (for the main client interface) and at
<http://<hostname>/webadmin> (for the administration interface).

Note that the OMERO web application does not seem to support being
published at any other place than the server root ("/"). If your
httpd server has another purposes beyong OMERO.web, you may want
to use a VirtualHost; in that case, include the OMERO.web
configuration inside a <VirtualHost> directive as follows:

<VirtualHost server_ip:80>
ServerName server.hostname

...insert the above-mentioned configuration stanza...


There are three different items to backup:

- configuration settings in /etc/omero/;

- 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 \
/OMERO /backup/

To restore, copy the configuration and data files back to their
locations and reload the database from the SQL dump.


For general informations about upgrading OMERO, see:

To upgrade OMERO 4.3.x to OMERO-4.4.x:

- stop OMERO if it is running;

- backup the SQL database;

- upgrade the package;

- upgrade the database:

$ cd /opt/omero
$ psql -h localhost -U omero omero < sql/psql/OMERO4.4__0/OMERO4.3__0.sql

- check config files in /etc/omero; remove old config file
/etc/omero/grid/default.xml and apply new settings:

# /etc/rc.d/rc.omero init

- start the upgraded server:

# /etc/rc.d/rc.omero start