Hey,

So my friend is a biochemistry guy, and was unable to install and run the application according to your instructions, since they assume some significant computer science knowledge.

I helped him out by putting together some installation instructions that work for macOS. They might be useful to add to your README.md. Feel free to modify them however you wish.

Installation Instructions

1) Start a terminal session

Git and Homebrew Stuff

2) Check that you have git installed:

$ git --verison

If so, move on to 3).

If not, move on to 2)a).

2)a) Check that you have homebrew installed:

$ brew --version

If so, move on to 2)c)

If not, move on to 2)b)

2)b) Install homebrew:

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

Move on to 2)c)

2)c) Install git with homebrew:

$ brew install git

Move on to 3)

3) Create and enter some new directory, for example:

$ mkdir ~/test
$ cd ~/test/

4) Clone and enter the project:

$ git clone https://github.com/pfred/pfred-gui.git
$ cd pfred-gui

Java Stuff

4) Check that you have Java installed:

$ java -version

If so, move on to step 5)

If not, move on to step 4)a)

4)a) Install Java with homebrew:

$ brew install java

Move on to step 5)

Ant Stuff

5) Install ant by clicking this link

6) Move the .zip file to ~/test/, unzip it, and delete the .zip file:

$ mv ~/Downloads/apache-ant-1.10.11-bin.zip ~/test/
$ unzip apache-ant-1.10.11-bin.zip
$ rm apache-ant-1.10.11-bin.zip

7) Find Java's filepath, and set JAVA_HOME to Java's filepath (the output of the first command):

$ /usr/libexec/java_home
$ export JAVA_HOME=<java's_filepath>

8) Set ANT_HOME to Ant's filepath:

$ export ANT_HOME=~/test/apache-ant-1.10.11/

9) Add Ant's bin directory to your PATH:

$ export PATH=${PATH}:${ANT_HOME}/bin

10) Get the library dependencies of most of the Ant tasks that require them:

$ cd ${ANT_HOME}
$ ant -f fetch.xml -Ddest=system

Final Touches

11) Modify lines 13 and 14 of ~/test/pfred-gui/build.xml:

$ open build.xml

In the text editor that appears, change lines 13 and 14 so that they look like this:

    <property name="compile.target"      value="1.7" />
    <property name="compile.source"      value="1.7" />

(Basically replace 1.6 with 1.7)

12) Compile PFRED:

$ cd ~/test/pfred-gui/
$ ant jar

13) Run PFRED:

$ ant run

For The Future