> For the complete documentation index, see [llms.txt](https://evolvingparasites.gitbook.io/evolvingparasites/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://evolvingparasites.gitbook.io/evolvingparasites/documentation/geneious.md).

# Geneious

A lot of members of the institute are using a software called *geneious* to analyse DNA-data. We have 6 licenses which are only compatible with the version 6.1.8 (you can get this old version [here](http://www.geneious.com/previous-versions/)). The server providing the licenses is *Harriet*. Additionally to the license server, Harriet is running a mysql server, which provides the *shared database* for all geneious-users at the institute.

## Setting up a Geneious client

### macOS

1. [Download the macOS-client.](https://assets.geneious.com/installers/geneious/release/Geneious_mac64_6_1_8.dmg) Double click the *.dmg* to mount it.
2. Copy the Geneious.app to your Applications directory. Start Geneious. At the window which popped up click *Activate a license*. Click on *Use floating license server*. Now enter the credentials you got from the administrator.

### Windows

1. [Download the Windows-client](https://assets.geneious.com/installers/geneious/release/Geneious_win64_6_1_8_with_jre.exe)
2. Double click the .exe and click through the installer. When it’s finished start Geneious, a window will pop up. Click on *Activate a license*. Click on *Use floating license server*. Now enter the credentials you got from the administrator.

### Linux

1. [Download the Linux-client](https://assets.geneious.com/installers/geneious/release/Geneious_linux64_6_1_8_with_jre.sh)
2. Run it with: `sudo bash ~/Downloads/Geneious_linux64_6_1_8_with_jre.sh` and click through the suggested parameter.
3. Now type *geneious* into the search and start it. At the window which popped up click *Activate a license*. Click on *Use floating license server*. Now enter the credentials you got from the administrator.

## Log into the shared Database

1. Start Geneious and right click onto **Shared Database** on the left hand side and click **Connect to a set up database**.
2. Type into the username, password, Host. The database-name is **geneiousDB** and the **Port 3306**. For the database vendor choose MySQL. Then click on **More Options** and click the **Browse** button behind “Driver .jar file:” choose [this file](https://github.com/majuss/ecoevolpara/raw/master/source/appendix/various/geneious/mysql-connector-java-5.1.30-bin.jar).
3. Click “Ok”, you are now connected to the shared database.

## Set up the Geneious License Server (Harriet)

This Tutorial will guide you from the start to set up the geneious license server on a completely new machine. It requires you in the first place to create a virtual machine with Debian Jessie. Jessie because in the later releases, software which is required by the geneious license server was removed from Debian. So you need an Debian running a 3.X Kernel. It is recommended [to use a virtual machine](https://majuss.gitbooks.io/ecoevolpara/Documentation/vms.html#stable).

Inside of the Debian stable VM you need to download the server software:

```
wget http://www.geneious.com/installers/licensingUtility/2_0_3/GeneiousLicenseServer_linux64_2_0_3_with_jre.sh/
```

Then start the script with root priveleages. During the installing process you will be asked for the license key. It is located in our KeePassX-database. All other option can be left at default. The license-server is now installed in `/usr/local`

## Setup the mysql database-server

export the old database

import it

set some value higher

`https://support.rackspace.com/how-to/installing-mysql-server-on-ubuntu/`