Installation

Install using the .deb or .rpm package from the command line using:

sudo dpkg -i snapgene-server_1.0.1.deb

(or whatever version is being installed). Likewise for rpm packages.

The installation directory is /opt/gslbiotech/snapgene-server. For this document we will refer to this directory as $EXEDIR.

New versions can be installed directly over old versions as long as the server is not running. Run $EXEDIR/stop before installing to ensure the server is completely shutdown first.

Other Prerequisites

See script $EXEDIR/install/install_ubuntu and install_fedora for the libraries and other changes required to run the server successfully.

Note that the install scripts install "ms core fonts" which requires the user accept a license agreement interactively. This can cause problems for automated installers. See this link for information on how to install "ms core fonts" without using the keyboard.

Snapgene server uses the zmq library for interprocess and intra-net communication within a server environment. The snapgene-server executable is written in C++ and the libzmq.so.3 shared library is installed automatically into the executable directory. The server also makes use of python scripts that require the python zmq package to be installed. The Debian package is named python-zmq.

Snapgene server can run as a separate restricted system user. The installation assumes the name "snapuser". See bash script install_ubuntu for the command line to create the user. The script also creates a group named "snapuser" but this can be changed by IT to aid file permissions when making file specific requests to the server. The name "snapuser" can be changed too as long as the ss-start script is updated as well.

Snapgene server requires some X window system to generate SVG maps and make font measurements. Headless servers typically do not have xserver installed. To fix this xvfb can be installed which is a lightweight virtual replacement for xserver. See install_ubuntu for the typical installation of this. xvfb does not need to startup at boot time because the software uses xvfb-run which starts an isolated xvfb session for a specific executable.

Configuration File

Before starting the snapgene server the main configuration file can be modified to control the number of daemons and the TCP ports they open. This file is in /etc/snapgene-server.conf.

Each daemon has a given "server index" from 1 to 100. For each index the tcp port can also be changed. Use enable=0 to disable the server index without removing the entire configuration section from the file.

Example Files

There are example files at /opt/gslbiotech/snapgene-server/examples.