Install the prerequisites¶
The HRM requires a few prerequisites for its functions.
Operating system¶
The HRM should work on any recent Linux distribution, but we only support Ubuntu (with its derivatives) and Fedora (that will apply to RHEL and CentOS). Distribution-specific differences are marked in the following with the corresponding distribution logos.
Warning
Please notice that with release 3.1, we dropped support for Mac OS X. HRM 3.0 is still known to work on Mac OS X from 10.5 (Leopard) onward, but no effort will be made to make future versions of the HRM compatible with Mac OS X. Also notice that the HRM was never tested on Mavericks. For reference, see the old documentation.
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¶
sudo apt-get install apache2
sudo yum install httpd
Web pages can be installed globally or per-user.
The Apache2 global document root is /var/www, or /var/www/html in more recent versions (14.04 LTS and newer).
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 set the AllowOverride directive in /etc/apache2/sites-available/default to enable .htaccess files in the HRM on the web server (AllowOverride All), or at least make sure to prevent access to the subdirectories inc, config, run, resources and setup.
If you are installing the HRM in your user dir, make sure to change AllowOverride to All in /etc/apache2/mods-available/userdir.conf (make sure to enable the userdir mod first by running sudo a2enmod userdir in the shell).
See also Enabling use of Apache htaccess files.
PHP ≥ 5.3¶
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 5 module for Apache2, the queue manager requires the PHP 5 command line interpreter.
Note
Minimum required PHP version is 5.3.
sudo apt-get install libapache2-mod-php5 php5 php5-cli php5-common php5-json
Note
JSON support for PHP was moved into a separate package php5-json in Ubuntu 14.04LTS; in older versions, JSON support is part of the core php5 package.
sudo yum install php php-cli php-common php-process php-json
A relational database¶
The HRM officially supports two relational databases: MySQL and PostgreSQL.
MySQL¶
sudo apt-get install php5-mysql mysql-server
sudo yum install php-mysql php-pdo mysql-server
Note
It is recommended to install a database management tool like phpmyadmin.
PostgreSQL¶
sudo apt-get install php5-pgsql postgresql
sudo yum install php-pgsql postgresql-server postgresql-contrib
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:
(Optional) LDAP support¶
If you plan to configure the HRM to use either Active Directory authentication or LDAP authentication, you will need to install the php-ldap package as well:
sudo apt-get install php5-ldap
sudo yum install php-ldap
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...
sudo apt-get install postfix
sudo yum install postfix
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.
sudo apt-get install zip
sudo yum install zip
(Optional) OMERO support¶
If you plan to use the OMERO connector, you will need to install the prerequisites for OMERO and download and unzip the OMERO command line client.
Note
It is NOT required to do any installation or configuration of the downloaded OMERO package! The HRM just needs this package for being able to communicate with your OMERO server, which can be installed on any machine that you can establish a network connection to (from your HRM server).
For the command line client, you need to download the “server” package from the OMERO website that matches your OMERO installation and the Ice version installed on your HRM system. As an example, the commands for OMERO 5.0.3 and Ice 3.4 are shown below, for other combinations please have a look at the OMERO download site. We recommend placing the OMERO client into a subdirectory of /opt/OMERO.
sudo apt-get install python-zeroc-ice libicessl34
wget http://downloads.openmicroscopy.org/omero/5.0.3/artifacts/OMERO.server-5.0.3-ice34-b41.zip -O /tmp/OMERO.server.zip
sudo mkdir -pv /opt/OMERO
cd /opt/OMERO
sudo unzip /tmp/OMERO.server.zip
rm /tmp/OMERO.server.zip
sudo yum install ice-python
wget http://downloads.openmicroscopy.org/omero/5.0.3/artifacts/OMERO.server-5.0.3-ice34-b41.zip -O /tmp/OMERO.server.zip
sudo mkdir -pv /opt/OMERO
cd /opt/OMERO
sudo unzip /tmp/OMERO.server.zip
rm /tmp/OMERO.server.zip
Note
Due to an issue in OMERO up to version 5.0.4 the client tries to store and read its session files in a subfolder of the HOME directory of the user running the OMERO client - in our case the same one that is running Apache. This will fail on most standard installations due to the default directory permissions in Apache’s document root, therefore it is necessary to manually create this session directory and adjust the permissions accordingly.
sudo mkdir /var/www/omero
sudo chown www-data /var/www/omero
sudo chmod u+w /var/www/omero
Please contact us in case you’re trying to set up the OMERO connector on a Fedora system and you’re running into trouble there!