Install the prerequisites

The HRM requires a few prerequisites for its functions.

Operating system

If you have not yet read the conventions, please consult the Operating systems.

Note

For those who plan on using the (Optional) OMERO support it is strongly recommended to set up the HRM and OMERO using the same Linux distribution and version, simply to avoid Ice version incompatibilities, which will prevent the HRM-OMERO connector from working. Details can be found in the OMERO system administrator documentation.

PLEASE MIND: this does NOT mean you should install HRM and OMERO on the same machine! You should just run the same Linux installation on them.

Huygens Core

The HRM is an interface to Scientific Volume Imaging’s Huygens Core. Huygens Core is is a fully scriptable compute engine intended to run image processing and deconvolution jobs on large 64 bit multiprocessor servers in headless mode, i.e. without a specific graphical interface. The HRM provides such an interface for multi-user, batch access to Huygens Core.

Note

If the web and the processing server are not on the same machine, you will need an additional Huygens Core for the web server with a reader license (free of charge).

Apache2 web server

DebianRHEL

sudo apt install apache2

Web pages can be installed globally or per-user.

The Apache2 global document root is /var/www/html.

If you plan to install the HRM in a specific user directory, use /home/<hrm_user>/public_html.

Apache2 access handling

HRM uses .htaccess files to prevent access to configuration files. Make sure to configure Apache2 to use them by setting the AllowOverride and Require directives in configuration files.

DebianRHEL

/etc/apache2/sites-available/000-default.conf

If you are installing HRM in your user directory also put the directives in /etc/apache2/mods-available/userdir.conf Make sure to enable the userdir mod first by running the follwing line in the shell:

sudo a2enmod userdir

See also Enabling use of Apache htaccess files.

Please notice that the Require directive is required from Apache version 2.4. Here is the code snippet for the config files

<Directory /var/www/html/hrm>
    Options Indexes FollowSymLinks
    AllowOverride All
    Require all granted
</Directory>

PHP

Note

Minimum required PHP version is 8.1.

The HRM is made of two parts, a web interface and a queue manager, both written in PHP but with different requirements. The web interface requires the PHP module for Apache2, the queue manager requires the PHP command line interpreter.

DebianRHEL

sudo apt install \
    libapache2-mod-php \
    php \
    php-cli \
    php-common \
    php-json \
    php-xml \
    php-ldap \
    php-mbstring

Note

When installing a PHP version that is not the default of your system it might be necessary to specify for which PHP version the packages are needed. Change php to for example php8.1 in the packages to get the packages for PHP 8.1. It might also be necessary to change the PHP version Apache2 uses with the a2dismod and a2enmod commands.

Production php.ini settings

Please configure the HRM machine for production. Edit the php.ini configuration file

DebianRHEL

/etc/php/8.1/apache2/php.ini

In there set at least the values below (more information can be found in the php.ini file itself).

display_errors = Off
display_startup_errors = Off
error_reporting = E_ALL & ~E_DEPRECATED & ~E_STRICT

A relational database

The HRM officially supports two relational databases: MySQL and PostgreSQL.

MySQL

DebianRHEL

sudo apt install php-mysql mysql-server

Note

It is recommended to install a database management tool like phpmyadmin.

PostgreSQL

DebianRHEL

sudo apt install php-pgsql postgresql

You will need to manually enable PostgreSQL:

sudo systemctl enable postgresql

Note

It is recommended to install a database manageent tool like phppgadmin.

Some additional information:

• This is a good tutorial from the Ubuntu Community on how to set up PostgreSQL to use with the HRM.

Disable SElinux

HRM needs access to several operations that are blocked by SElinux.

DebianRHEL

By default SElinux is disabled. In case SElinux has been enabled edit file /etc/selinux/config and update the following variable.

SELINUX=permissive

Note

Restart the machine after changing the value of SElinux.

Sendmail (postfix)

HRM uses the PHP mail() function to notify the users:

“For the Mail functions to be available, PHP must have access to the sendmail binary on your system during compile time. If you use another mail program, such as qmail or postfix, be sure to use the appropriate sendmail wrappers that come with them.” More…

DebianRHEL

sudo apt install postfix

Note

If your mail server is set up correctly and still PHP cannot send e-mails, SELinux might be blocking it. Query the status of httpd_can_sendmail as follows:

$ /usr/sbin/getsebool httpd_can_sendmail

If httpd_can_sendmail is off, you can enable it with:

$ /usr/sbin/setsebool -P httpd_can_sendmail on

PHP date() and default timezone

Please make sure to set the default timezone in php.ini as follows:

[Date]
; Defines the default timezone used by the date functions
; http://php.net/date.timezone
date.timezone = "Europe/Zurich"

Otherwise you will get the following warning every time the PHP function date() is called within the HRM:

PHP Warning: date(): It is not safe to rely on the system's timezone settings. You are
required to use the date.timezone setting or the date_default_timezone_set() function. (...)

Click here for the full list of supported time zones.

SSH

If the queue manager and the image processing server are not on the same machine (see installation instructions), HRM transfers files via ssh between the two using sudo. To allow HRM to login and run commands as sudo via remote, it is necessary to comment out the line 'Defaults requiretty' in the /etc/sudoers file.

Compressors

The HRM compresses files to be downloaded (such as deconvolution results). Several options are possible (and more can be added in the configuration files), but by default the HRM uses zip.

DebianRHEL

.. code-block:: sh

    sudo apt install zip

(Optional) OMERO support

For using the OMERO connector, you will need to install the corresponding Python package. Please refer to the HRM-OMERO Connector project for installation details.