Some SlackBuild scripts for Slackware.
You can not select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.

7.6 KiB

                 PACKAGER'S README FOR OMERO-5.0.5

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 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 `' 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 `' in the
OMERO configuration.

Note that OMERO 5.0.0 needs another directory, defined by the key
`omero.managed.dir'. In the default configuration file, this key
uses the value of the `' key as follows:

but OMERO then complains that `' is undefined, so you
should really specify a full path for `omero.managed.dir`, even if
the directory is located below ``:


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 `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 /data/omero

Parameters may also be defined in a `/etc/omero.conf` files, using
the same format as the `` 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/' does not exist on the
server). This initialization step should be performed each time the
`/etc/omero.conf` 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:


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

are 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 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 \
/OMERO /backup/

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 4.4.x to OMERO-5.0.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/OMERO5.0__0/OMERO4.4__0.sql

- start the upgraded server:

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