Quick Start Guide

What is SnapGene Server

SnapGene Server is an application you can install on a web server in order to generate interactive or static DNA maps on your website. In addition to generating maps, you can also do the following:

  • Convert any format supported by SnapGene to the .dna file format
  • Convert .dna files to FASTA or GenBank format
  • Annotate a sequence by detecting common features
  • Annotate primer binding sites by importing primers from a list
  • Export a feature summary
  • Export a primer summary

See https://www.snapgene.com/snapgene-server for an overview.

Install SnapGene Server

Visit https://www.snapgene.com/my-account/ and login to download the appropriate package for your Linux distribution. At this time SnapGene Server supports Fedora Linux 23+ and Ubuntu Linux 14+.

To install on deb based distributions (e.g. Ubuntu):

sudo dpkg -i /path/to/snapgene-server.deb

cd /opt/gslbiotech/snapgene-server/install

sudo ./install_ubuntu

 

To install on rpm based distributions (e.g. Fedora):

sudo dnf install /path/to/snapgene_server.rpm

cd /opt/gslbiotech/snapgene-server/install

sudo ./install_fedora

Add PHP ZMQ Support

It is necessary to add PHP ZMQ support to Apache to be able to communicate over ZMQ between a PHP powered web page and the SnapGene Server daemon.

To install on deb based distributions (e.g. Ubuntu):

apt-get install -y python-zmq

pecl install zmq-beta

 

To install on rpm based distributions (e.g. Fedora):

dnf install zeromq-devel

pecl install zmq-beta

 

Next, edit /etc/php.ini and add

extension=zmq.so

 

Finally restart Apache so that the ZMQ extension is loaded.

apachectl restart

 

The extension should have been installed under: /usr/lib64/php/modules.

You can verify that ZMQ support has been loaded by calling “phpinfo()” from any .php code.

Activate SnapGene Server

Before SnapGene Server can run it needs a license installed. Request and install a license like so:

sudo /opt/gslbiotech/snapgene-server/tools/license-utility.py -t requestLicense -n "GROUP NAME" -c "REGISTRATION CODE"

 

If things work as expected, your license file should be installed under:

/etc/snapgene-server/.klf

 

Alternatively, you can check the license status like so:

sudo /opt/gslbiotech/snapgene-server/tools/license-utility.py -t info

Start SnapGene Server

sudo /opt/gslbiotech/snapgene-server/tools/start

 

Finally, verify that SnapGene Server is running:

/opt/gslbiotech/snapgene-server/tools/info.py

 

If desired, you can stop SnapGene Server like so:

sudo /opt/gslbiotech/snapgene-server/tools/stop

 

Adding start to your distributions startup script to ensure the daemon is started automatically is left as an exercise to the reader.

Additional Reading

See /opt/gslbiotech/snapgene-server/example.php for an example of how to dynamically generate map content from a web page.

To learn how to take advantage of the full set of functionality, read the full manual installed under:

/opt/gslbiotech/snapgene-server/SERVER_MANUAL.txt