genesis2

User manual

Documentation for building on other platforms

JAR files for MacOS, Windows and Linux are available. This section provides instructions for other platforms

A build on another platform should work, subject to checking that the right dependences for JavaFX libraries are used. The way the project is set up, Maven should automatically find them.

Configuration concerns

To run the version that does not include dependences on the command line, you need to download a version of the JavaFX SDK.

Assuming the JavaFX library is in directory named in shell variable $JAVAFX and your JAR file is in $JARF, you can invoke it as follows:

java --module-path $JAVAFX --add-modules javafx.controls,javafx.fxml,javafx.swing -jar $JARF

Note: the library path should go to the actual contents so if e.g. the path is /usr/local/lib/JavaFX/lib then include the trailing part of the path after /lib. In my examples, the libraries are not in another layer of lib directory as this is implied by the rest of the path.

There is a Bash script genesis.sh in this repository (in scripts) that can run the above. To invoke, create environment variables that the script will use (it has defaults if you don’t do this). To the the above effect (modifying the paths to suit your install):

export JAVAFX=/usr/local/lib/JavaFX-21
export JARF=$HOME/Applications/Genesis2-2.4b-Generic.jar

Note: in Unix shell scripting, you can create a shell variable wuthout using the word EXPORT but the value will not be visible to a child process, i.e., the script will not see it. The JavaFX path should contain the actual library files – if they are in a directory called lib append that to the path.

Building on different environemts

• Install git if you don’t have it already; there are versions for all Unix platforms (including Mac) and Windows
• On the command line (assuming you want this branch), run git clone -b Philip https://github.com/h3abionet/genesis2.git
• Install JDK (21 is tested; earlier versions may work) – make sure you get the right version for your platform
  • For a Mac, you want the DMG installer for ARM (if your machine is an M1, M2, M3, etc, model, x64 otherwise)
  • For Linux, whether you want a DEB or RPM depends on the Linux distribution (also there are options for both ARM and x86; for Linux x86 is more common)
  • For Windows, either the .exe or the MSI installer should work
• Install NetBeans (version 18 includes a Mac installer, though 19 can also run on all platforms)
• Install SceneBuilder if you want to edit the user interface
• Open Netbeans, select Open Project and navigate to the place you downloaded using git – the top-level directory (folder) should be called genesis and NetBeans will recognize this as a project
• Look for Clean and Build under the Run menu, or the clean and bulid icon (hammer and broom) and select either of them.
  • Look in the target directory (folder); you should find two JAR files:
    • the one with the name ending with with-dependencies.jar should be possible to launch from the file browser (Finder on a Mac)
    • the other JAR file does not include the JavaFX libraries and should be possible to launch from the command line using the genesis.sh script (or a variation suitable for Windows)

Test data

Data to test functionality is available in the repository in directory agm-demo/agm-genesis/sample-data/ (Windows users can rotate the slashes to suit).

Data file types available to open are:

• .g2f – a Genesis2 project (the first thing to open, unless you want to start from scratch); you can then use
  • .eigenvec – PCA file
  • .Q – Admixture file
    • when opening one of these, you are not restricted as to file type as there is no standard for admixture files
    • this will add another pane to graph the admixture plot
    • you can open more than one admixture file and there will be an additional plot for each
• If you start a new project instead, you need to add the following file types:
  • .fam – a FAM file
  • .phe – phenotype file
  • You will also need to import a PCA file (.eigenvec) before anything is graphed

This site is open source. Improve this page.