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¶

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 configure Apache2 to use them by setting the AllowOverride and Require directives in configuration files.

/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

/etc/httpd/conf/httpd.conf

If you are installing HRM in your user directory also put the directives in: /etc/httpd/conf.d/userdir.conf

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 5.5.

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.

sudo apt-get install libapache2-mod-php5 php5 php5-cli php5-common php5-json php5-xml

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 php-xml

Production php.ini settings¶

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

/etc/php5/apache2/php.ini

/etc/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¶

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:

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

(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

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.

sudo apt-get install zip

sudo yum install zip

(Optional) OMERO support¶

If you plan to use the OMERO connector, you will need to download the “server” package from the OMERO website that matches your existing OMERO installation and the Ice version installed on your HRM system. To make it work on your system, you also need Python 2.6 or 2.7 and (which is installed by default on Fedora and Ubuntu) and Java 7.

Warning

The connector requires at least the 5.0 series of OMERO, the latest version is only tested against OMERO 5.1 and newer!

Note

It is NOT required to do any installation or configuration of the downloaded OMERO package! HRM just needs this package to communicate with your existing OMERO server. Thus, this package allows HRM to communicate with any OMERO server connected to the network.

Required OMERO Connector Components¶

This section explains the steps required if you want to use the optional OMERO connector.

As an example on how to download these packages, the commands used to fetch 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 downloaded OMERO “server” package into a subdirectory of /opt/OMERO, as follows:

sudo apt-get install python-zeroc-ice libicessl34 openjdk-7-jre
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 java-1.7.0-openjdk
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

From HRM 3.3.0 on, the OMERO connector requires the Python package argparse, which is included by default from Python 2.7 on. In case you are running an older Python version, you have to install the package yourself. Please refer to the installation instructions of your distribution on how to set up Python argparse.

Please follow the instructions in configuring the OMERO connector about the optional configuration variable PYTHON_EXTLIB in case you have to place the package in a non-default location.

This configuration variable also applies to the following section!

Additional Python Packages (Optional)¶

This section is about packages that are not mandatory for using the connector, but add more functionality to it.

If the Python Imaging Library (PIL) or Pillow is installed, the connector will download thumbnails as well to use them as previews in the HRM side bar. Those “simple” previews can of course be replaced with the HRM ones by clicking on the “Re-generate Preview” link.

In case the Beautiful Soup library is available on the system, the connector will generate parameter summaries and attach them as a human-readable comment to any image uploaded to OMERO.

sudo apt-get install python-imaging python-bs4

sudo yum install python-imaging python-beautifulsoup4