Advanced Administration

Default data location

By default, the data location will be in the user's home directory. You can change this by setting an environment variable which will be used by the Geneious Prime launcher such as setting a $HOME$ variable to be where you want a user to store their data.

On Windows and Linux, edit the Geneious.in.use.vmoptions file in the installation directory, and add -DdataDirectoryRoot=$HOME$/Geneious on a new line after the other settings.

On Mac OS X, edit the /Applications/Geneious\Prime.app/Contents/Info.plist and find the <key>Arguments</key> section to match the following:

<key>Arguments</key>
<string>-distributionVersion
-DdataDirectoryRoot=$HOME$/Geneious</string>

A special $JAVA_USER_HOME$ variable is normally used which resolves to user.home and is what Geneious uses by default. The program will create a Geneious Data folder inside the directory you specify.

If you wish to hide the local folders and force users to use only the Shared Database, edit the geneious.properties file by removing the # before the line show-local-database=false.

Change default preferences

Change preferences within Geneious Prime

Start a fresh copy of Geneious Prime, set it up the way you want. Shut down and then copy the file Geneious Data/user_preferences.xml.

On Windows and Linux, copy the file to the Geneious installation directory and rename it to default_user_preferences.xml.

On MacOS rename the file to default_user_preferences.xml and copy it to either /Users/(username)/Library/Application Support/Geneious/ (to set preferences for a single user account) or /Library/Application Support/Geneious/ (to set preferences for all users of a computer)

The default preferences set for all users of a computer will take precedence over default preferences set for individual users.

After copying the default_user_preferences file to the appropriate location, when users start Geneious Prime for the first time they will get the configuration you set rather than the normal default.

Examples of features you can change:

  • Turn off automatic updates

  • Set default custom BLAST location

  • Set up a shared Database

  • Set up a proxy server default

  • Turn off particular plugins

Any users who have already run Geneious should click the "Reset All Preferences" button in the Geneious Preferences to load these defaults.

geneious.properties file

Any preferences which can be set within Geneious Prime can also be set from the geneious.properties file which can be found in the Geneious Prime installation directory. On MacOS this file is located in Geneious Prime.app/Contents/Resources/app (Prime 2021.1 and later) or Geneious.app/Contents/Java (Prime 2021.0 and earlier).

Note that on MacOS this file should be copied to an external location before it is edited. Modifying this file directly in the application bundle will break its app signature, which may have unintended side effects such as intermittent application crashes. The file should be copied to either /Users/(username)/Library/Application Support/Geneious/geneious.properties (to set properties for a single user account) or /Library/Application Support/Geneious/geneious.properties (to set properties for all users of a computer)

Properties defined for all users take priority over properties defined for individual users.

Some examples of how to modify geneious.properties are present in the file already - remove the hashes from the start of the lines and modify the values to use them. If you need to find out how to set other preferences using this file, please contact Geneious support.

It is also possible to turn off access to all external services by editing this file (this is not possible via the preferences inside Geneious). This includes access to NCBI, Uniprot, Geneious plugin download, submission of error reports, support requests and usage tracking.

Pre-configuring Shared Database connections

The Shared Database connection settings can be set in the geneious.properties file so that users do not have to enter these settings in Geneious. The properties to set depend on the connection method used.

Create Direct SQL Connection through geneious.properties

Open the geneious.properties file and scroll down to ##database configuration , and enter the details for database-host (the host running the database server), database-dbname (the database name) and database-type (one of "MYSQL", "POSTGRESQL", "SQL_SERVER" or "ORACLE"). These three fields are required for the connection to work. You must also specify the location of the database-driver if using MySQL; this field is optional with the other database servers. The optional property database-user will be used if provided. Remove the # at the start of these lines for these settings to be used.

Create Geneious Server Database connection through geneious.properties

Open the geneious.properties file and scroll down to ##Geneious server connection and enter the url for gserver-host (the host in which Geneious Server is running). Other optional properties that can be provided are gserver-ssl ("true" to use SSL), gserver-context (Geneious Server context to use) and gserver-port (port to connect). If any of these optional properties are not provided then the default values will be used. Remove the # at the start of these lines for the settings to be used.

Pre-configuring license information

License information can be preset in the geneious.properties file so that users do not need to enter this themselves.

Personal or Group licenses

Open the geneious.properties file in a text editor and scroll down to ##provide a flexnet-local license key (except trial). Remove the # next to license-key= and add your license key.

Floating licenses

Scroll down to ##license server settings, and change override-property-flexnet_server.host and override-property-flexnet_server.port to the settings you require. Remove the # at the start of these lines for the setting to be used. This setting cannot be used to configure Sassafras KeyServer licenses.

Adding custom plugins to the Plugins menu in Geneious Prime

Administrators can add custom, in-house plugins to the Plugins menu in Geneious Prime, and restrict access to publicly available plugins by doing the following:

  1. Set up an XML file that contains information for each plugin you want to add, including its name, description, version information, and a URL from which Geneious can download it. For an example of the format to use, see https://desktop-links.geneious.com/assets/plugins/DownloadablePlugins.xml

  2. Go to Tools → Preferences → General, and click "Advanced...". Look for the advanced preference CustomPluginXmlUrl. Select it, click Edit and enter the address of the XML file you created. This can be a link to a web server hosting the XML file, or can be a link to a file in the format file://<host>/path/to/file, which is installed at a known accessible location on local or shared disk. You must restart Geneious to apply the changes.

Geneious uses the contents of the XML file to add the custom plugins to the Plugins menu in Geneious. All available plugins from Biomatters will still be displayed, along with the additional plugins from the custom XML file. The xml file is also used to determine when to notify the user that a new version of a plugin is available to download.

If you wish to turn off access to the Biomatters-provided plugins, so that only the custom plugins are visible, use the Advanced Preference DisableCheckForBiomattersPluginUpdates and change this to "true", then restart Geneious. If you wish to restrict network access to the outside or control which Biomatters-provided plugins are available, you can locally mirror the Biomatters plugins you want to provide, and use a custom XML file to specify the details.

Deleting built-in plugins

Features of Geneious Prime can be turned off in preferences as described in the section above on changing default preferences. If you really want to delete a feature completely so your users can't reinstate it you should shut down Geneious Prime, go to the installation directory, into the bundledPlugins directory and delete the desired plugin jar files/folders.

Max memory

On Windows and Linux, edit the files Geneious.default.64bit.vmoptions and Geneious.in.use.vmoptions in the installation directory and change the -Xmx value to your preferred setting.

On Mac OS X, edit the /Applications/Geneious.app/Contents/Info.plist file and find the VMOptions section and modify the -Xmx setting.

Note that Geneious will automatically allocate the maximum available RAM so it is not normally necessary to alter this setting.

Web Linking to Data in Geneious Prime

It is possible to create web links which will open data in Geneious Prime when they are clicked in another program. This only works on Windows and Mac OS and Geneious Prime has to be installed on the machine where the link is clicked. Note that some browsers (including Safari on MacOS) may not support these type of links.

There are two types of links supported:

(1) A link which will download and import a file from a given location into Geneious Prime. To do this, use the following form of URL:

geneious://file=<PathToFile>

For example, to download and import the pET15-MHL vector from the Addgene Plasmid Repository, use: geneious://file=https://media.addgene.org/snapgene-media/v1.7.9-0-g88a3305/sequences/12250/9998fdbe-051f-4dc6-ba0f-24e65127a0c5/addgene-plasmid-26092-sequence-12250.dna

To open a file in a local folder, use the following format: geneious://file=file:///C:/Users/Your_name/Desktop/file_name

The file can be of any format which Geneious Prime is able to import (see Data Input Formats), including plugin format. Only one file can be linked to in this way.

(2) A link which will select documents which are already stored in Geneious Prime, either in your local folders or a Shared Database. To do this, use the following form of URL:

geneious://prime/documents?urn=\<URNofDocument>

or to select several documents:

geneious://prime/documents?urn=\<URNofDocument1\>&urn=\<URNofDocument2\>

To find the URN of a document, click on the small column selector button at the top-right corner of the document table and enable the URN column. You can then right-click on the URN of a document in the table and choose Copy URN.

For documents in the Shared Database, you can automatically create a web link to a document by right clicking on the document and going Copy link to Document. This can also be performed for multiple selected documents. The full web link (not just the URN) will then be copied to the clipboard. If the link is opened or clicked in another program, such as a web browser or chat program, Geneious Prime will automatically open with these documents selected. The link can also be pasted into the search box in Geneious to quickly find the document. Anyone who has access to the same Shared Database can use the link.