1 Client/server architecture
2 Installing the SeqSphere+ Server
- 2.1 Server Installation on Microsoft Windows
  - 2.1.1 Installation as Windows Service
  - 2.1.2 Installation as Application
- 2.2 Server Installation on Linux
3 Installing the SeqSphere+ Client
- 3.1 Client Installation on Microsoft Windows
- 3.2 Client Installation on Linux
4 Connecting and Initializing the Server
5 Customizing the Server

Client/server architecture

Ridom SeqSphere+ consists of a client application and a server application:

The SeqSphere+ Server has an integrated SQL database and can be connected by SeqSphere+ clients via LAN or internet.
The SeqSphere+ Client is a desktop application that must be installed on your local computer.

The client/server architecture allows distributed workgroups to cooperate via intra- or internet. Multiple users can access the data from various computers. Access rights and privileges can be configured to restrict access for specific users or groups.

For a single user scenario both applications may be installed on the same computer.

Important: Please be sure to check System Requirements before installing.

Installing the SeqSphere+ Server

Server Installation on Microsoft Windows

The Ridom SeqSphere+ Server can be installed in two modes:

as Windows service that is started automatically when Windows start up and runs in the background as long as Windows is running, independent of the current Windows user.
as plain application that must be started by a user, and is terminated when the Windows user signs out.

If multiple users should be able to access the same server via intra-/internet, the second option (installation as background service) is recommended to ensure that the Server always will be running independent from the logged-in user. If multiple Windows users of the same computer should be able to access the same server, the second option (installation as background service) is required because the installation of the Ridom SeqSphere+ Server as ordinary program for various Windows users of the same computer would require multiple Server activations that are not allowed by the licensing model.

Start the installer executable and follow the messages of the installation wizard dialog. During the installation process it is possible to select if installation as service should be done.

Installation as Windows Service

SeqSphere service status window

If installation as service is selected, a working directory must be chosen were the software stores the database, configuration, and logging files (default C:\seqspheredata). It is not recommended to choose a network location for this directory.

A service with the name "seqsphereserver" is installed and automatically started. Therefore, the Ridom SeqSphere+ Server is already running when installation is finished. The Windows menu entry Ridom SeqSphere Server > SeqSphere Status can be used to Start and Stop the service.

Hints:

The setup configures the Windows firewall to allow remote access to the SeqSphere server. If another firewall is used make sure that the program seqsphereserver64.exe is allowed to open connections.
By default the service is started as Local System account. If the service needs to access a network drive (e.g., to store backups) the account must be changed to an ordinary user account. See Microsoft TechNet for a description how to do this.

Installation as Application

If not installed as a service, Ridom SeqSphere+ Server can be run by clicking the desktop icon or selecting the entry in the Start Menu. Ridom SeqSphere+ Server will create a working directory located in your home directory (e.g., C:\Users\<username>\seqsphere-server). This directory will contain the database, configuration, and logging files.

Hints:

If the server is installed and started as normal application (and not as service) then every Windows user that starts the server will work on an own SeqSphere+ database.
Note that on the first start of the server, the Windows firewall may show a security warning. Select "Allow access" in the security warning dialog.

Server Installation on Linux

Extract the installer package (tgz) into the directory where you want to install the SeqSphere+ server (e.g., with command 'tar xvzf RidomSeqSphereSERVER*'). By default, the server listens on port 8064, therefore this port must be excluded in a firewall. If the SeqSphere+ server should be used by multiple users, an installation as Systemd Service is recommended.

Start with graphical user interface (for single user usage)

Click or start in a terminal the shell script seqsphereserverGUI.sh in the extracted directory RidomSeqSphereServer. The database is by default located in the working directory .seqsphere-server/ of the home directory of the Linux user. So every user who starts the server will get his own database.

Start without graphical user interface

The run control script rcseqsphereserver.sh can be used to control the SeqSphere+ server:

./rcseqsphereserver.sh start' starts the server
./rcseqsphereserver.sh status' gives a status info for the running server
./rcseqsphereserver.sh stop' stops the server if it is currently running

The rcseqsphereserver.sh script can be called from any other directory and can be used to automatically start the SeqSphere+ server in a system init configuration. The working directory can be configured in the script file, default is .seqsphere-server/ in the home directory of the Linux user.

Installation As Systemd Service

The installation package contains the file seqsphereserver.service in the subdirectory /install/systemd. This file can be used to define a systemd service unit for the SeqSphere+ server. The following steps are recommended:

Step 1: Create a new user seqsphereserver (or change in service file)
Step 2: Extract the installation package into /home/seqsphereserver (or change in service file)
Step 3: Copy the file seqsphereserver.service into /etc/systemd/system
Step 4: Enable the service with: sudo systemctl enable seqsphereserver
Step 5: Start the service with: sudo service seqsphereserver start

If additional configurations (like port or working directory) should be specified, command line parameters can be appended to the ExecStart line in the service file.

Installing the SeqSphere+ Client

Client Installation on Microsoft Windows

Start the installer executable and follow the messages of the installation wizard dialog. Be sure to choose a local drive as installation directory, and not a network drive. The installer can also be started with command line options for an unattended installation.

After the installation procedure is completed Ridom SeqSphere+ can be run by clicking the desktop icon or selecting the entry in the Start Menu. Ridom SeqSphere+ will create a profile directory located in your home directory (e.g., a path like C:\Users\<username>\seqsphere). This directory will contain the configuration and logging files.

Important: Some SeqSphere+ client features (e.g., SKESA, Mash, AMRFinderPlus, or MOB-Suite) are only available on Windows after the installation of the Windows Subsystem for Linux.

Client Installation on Linux

Extract the installation package (.tgz) into the directory where you want to install SeqSphere+. (e.g., with command 'tar xvzf RidomSeqSphere*'). Then change into directory RidomSeqSphere and execute ./seqsphere.sh to start the application.

To use the automatic online update function the seqsphere process must have write permission for the installation directory.

The first time you start Ridom SeqSphere+, the software will create the profile directory .seqsphere in your home directory. This directory is used for the configuration files, logging files and pipeline scripts.

Important: Some SeqSphere+ client features (e.g., Chromosome and Plasmid Overview) are only working after the installation of Bioinformatic Tools on Linux.

Connecting and Initializing the Server

Step 1: Start SeqSphere+ server and wait until the server has started up.

Step 2: Start SeqSphere+ client.

Step 3: If SeqSphere+ server is not yet defined on your computer, the following startup dialog opens.

Step 4: If your SeqSphere+ server runs on the same computer, choose the first option Search Local SeqSphere+ Server, and confirm the found server with the button Use this Server.

If your server runs on a different computer choose Define Server Configuration, enter the Server Host name or IP address (port can be left empty to use the default port) and confirm with OK.

Step 5: If the server database has not been initialized before, a question dialog opens. Confirm with Yes.

Step 6: A dialog opens to define the Administrator account and a first user account. The Administrator is only meant for administrative usage. This account cannot be used to create new genotyping data. Therefore in addition a user account needs to be established too. For small (single user) installations, it is convenient to grant administrative rights to this user, too. Finally a name for the first user group must be entered. This group initially contains the Administrator and the first user.

Below the account section the paths for the database, the storage of uploaded assembly files, and the created backups can be defined. By default they are all stored in the server profile directory

Step 7: After the accounts are created a dialog opens to directly login as Administrator or as the defined user account. Further logins will require the entered password of course.

Step 8: The SeqSphere+ server requires a software license, otherwise it runs in a read-only mode. If no license is found, a dialog window opens to activate your license with a key that was delivered with the software, or to request a new license key from the Ridom website. The activation of the license requires an Internet connection. If the connection fails, please check the proxy settings.