hrm_installer

Set of bash scripts for the automated installation and configuration of the Huygens Remote Manager (HRM).

About

This set of Bash scripts guides you through the installation and configuration process of the Huygens Remote Manager (HRM). It installs all necessary dependencies, configures the web server, sets up the database, downloads the latest version of HRM and sets the required permissions, SELinux and firewall rules. The scripts may be used for quick installation of HRM and testing. However, for production use review and further configuration is recommended. In this case, please also read the HRM installation documentation.

Changelog

Version 0.3 (Nov. 2018):

• Added whiptail dialogs and a non-interactive mode

Version 0.2 (Jun. 2016):

• Updated scripts for Ubuntu 16.04 and CentOS 7

Version 0.1 (Jun. 2015):

• Initial release

Requirements

• Ubuntu 20.04+, Rocky Linux 8
• Superuser rights
• Internet connection
• HuCore installation and license

HuCore must already be running on the machine. The working installation can easily be tested by using the hucore command in a terminal window.

Usage

Go to the shell, change to the installation script's directory and run:

$ sudo ./setup.sh

Then follow the on-screen instructions and fill in your desired settings. When the installation has completed successfully, please reboot the computer. After that you may use HRM via your web browser on localhost at your chosen path,e.g. http://localhost/hrm/ . The default HRM admin account name and password are admin / pwd4hrm .

Detailed steps

These are the steps performed by the installation script in more detail. They are grouped under 7 different headings:

1. Installing system packages (step 1/7)
2. Configuring the database (step 2/7)
3. Installing HRM files (step 3/7)
4. Configuring HRM (step 4/7)
5. Configuring PHP (step 5/7)
6. Making the database (step 6/7)
7. Configuring the queue manager (step 7/7)

And under the hood, the following operations are performed:

1. Check for HuCore installation and get installation path.
2. Check for missing dependencies and try to install those packages. If a database management system, either MySQL/MariaDB or PostgreSQL, is missing you have to choose one.
3. Configuration of missing packages through system's package manager.
4. Creation of HRM's system account, database account and database for chosen DBMS. You have to provide or set account names and passwords.
5. Installation and configuration of HRM. The latest stable version will be downloaded or you may also offer an offline ZIP file of HRM. You have to provide the installation path and an image data storage path.
6. Setup of web server, configuring PHP, creating the database and running the HRM queue manager as system daemon.
7. Setting all necessary access permissions. The apache web server user will become member of the hrmgroup, the queue manager is run as hrmuser, and the image data storage directory's group is set to hrmgroup with sticky bit enabled. For Fedora and CentOS also the required SELinux and firewall rules are set.

Non-interactive mode and script modifiers

In non-interactive mode, the script can perform a complete installation without any user intervention. Simply add the --interactive=false flag to the command:

$ sudo ./setup.sh --interactive=false

The following default values will be used. However, any of those can be set via the command-line (e.g. --hrmtag="devel").

Variable name	Default value	Function
interactive	true	Interactive mode
debug	false	Some debug output
help	false	Very limited help
license	""	The hucore license string
dbtype	"mysql"	The database type ("mysql" or "pgsql")
dbhost	"localhost"	The database hostname
dbadmin	"root"	The database admin user
adminpass	""	The default admin password
dbname	"hrm"	The name of the HRM database
dbuser	"hrmuser"	The name of the database user for HRM
dbpass	"pwd4hrm"	The password of the HRM database user
sysuser	"hrmuser"	The system user that will run the HRM queue manager
sysgroup	"hrm"	The system group the of the HRM system user
apache_user	"www-data"	The apache user
hrmdir	"/var/www/html/hrm"	The location of the HRM website
hrmurl	""	The URL of the HRM website
hrmrepo	"https://github.com/aarpon/hrm.git"	The GIT repository used for pulling HRM
hrmtag	"latest"	The HRM tar or branch ("latest" is converted to the tag of the current release)
imgdir	"/data/images"	The folder HRM will use to store images and user data
srvimgdir	"/data/images"	File server base folder as seen from the Huygens server machines
hrmemail	"hrm@localhost"	The email address which will appear when HRM sends e-mails
hrmpass	"pwd4hrm"	The default HRM admin password
zippath	""	The path of a zip installation file which will be used instead of the GIT repository
postmax	"256M"	PHP post_max_size (limits POST size for browser uploads)
upmax	"256M"	PHP PHP upload_max_filesize (limits file size for browser uploads)
devel	false	Install the development version of HRM
rolling	false	Show GIT master (rolling changes) as an install option for HRM
bypass	false	This bypasses the license check in login.php (devel option to test the web interface)
remotedeconv	false	Set to true to deconvolve on a machine different that the one hosting HRM
srvhostname	"remote.server.com"	The name of the remote machine which deconvolves images
step		Launch a single step in isolation (1-7; by default, perform all 7 steps in sequence)

Script usage

Here are some ways in which the script can be used.

To run the script in non-interactive mode:

$ sudo ./setup.sh --interactive=false

To install the development version of HRM, use the following command:

$ sudo ./setup.sh -D

To install from a zip file (the path will be checked):

$ sudo ./setup.sh --zipfile="hrm_v3.4.0.zip"

To change the folder in which HRM will be installed:

$ sudo ./setup.sh --hrmdir="/var/www"

To change the email address HRM uses to communicate:

$ sudo ./setup.sh --hrmmail="hrm@valid.email.address"

Self decompressing script

For ease of use, setup.sh and the scripts folder can be packaged together into a single self-extracting bash script called hrm_setup. To build this file, just run build.sh.

The decompression script bundled with the self-extracting script (scripts/decompress.sh) assumes that the tar command is available on your system.

Authors and contact

Author of the HRM installation scripts:

• Torsten Stöter (torsten.stoeter@lin-magdeburg.de), Leibniz Institute for Neurobiology, Magdeburg
• Egor Zindy (egor.zindy@cmmi.be), Centre for Microscopy and Molecular Imaging, Gosselies

Further authors of the Huygens Remote Manager:

• Aaron Ponti, Department of Biosystems Science and Engineering, ETH Zurich
• Daniel Sevilla, Scientific Volume Imaging (Hilversum)
• Niko Ehrenfeuchter, Biozentrum (Basel)
• Olivier Burri, BioImaging and Optics Platform, EPFL (Lausanne)
• Frederik Grüll, Biozentrum (Basel)

Copyright and licensing

This software is copyright by the HRM developers (see above) and licensed under GPLv3.