newhybrids

This is the source code repository for the program newhybrids written by Eric C. Anderson. The old documentation which I have put into new_hybs_doc1_1Beta3.pdf here is mostly relevant.

I have only tested this on Macs.

Binaries

In bin/PC you will find newhybrids.exe which I compiled on a virtual PC (Windows 7) on my Mac, using Compile-with-no-gui.sh. You can download it and then do:

newhybrids.exe --help-full

for a full explanation of the command line syntax.

In bin/OSX you will find Mac OSX compatible binaries, newhybs and newhybsng, which are the versions with and without the GUI, respectively. You can download the whole repository from GitHub, then if you are on the Terminal in the top level of the repository you can do like this:

./bin/OSX/newhybs --help-full

for a full listing of options. If this seems mysterious, find a friend who knows their way around the Unix/Linux command line.

Building the program

Here are the basic steps to build this on a Mac. Note that you have to have the developer tools installed (install XCode for free from the app store). From the terminal do the following:

# first clone it from GitHub
git clone https://github.com/eriqande/newhybrids.git
cd newhybrids
git submodule init
git submodule update

# then configure it without-x for the Mac and make it
./configure --without-x
make

# the above makes two binaries:
# newhybs    : newhybrids with the GLUT interface
# newhybsng  : newhybrids with no GLUT interface


# at this point, if you want to install these into
# /usr/local/bin you can do this:
sudo make install 

Build it without autotools/make etc

The automake chain is something of a mystery to me, and that is only there for getting the GUI to work. If you are using it on a cluster, you won't want that anyway. In that case, just compile it with the simple script Compile-with-no-gui-Linux.sh. For example, from within the newhybrids directory, do this:

 ./Compile-with-no-gui-Linux.sh

That makes an executable called newhybrids-no-gui-linux.exe. You can get the help for it by doing this:

./newhybrids-no-gui-linux.exe --help

Command line interface

Newhybrids has a nicer command line interface now than it did before. To read about the available options you can do:

newhybs --help

# or

newhybs --help-full

# or if you are feeling fun you can do

newhybs --help-nroff | nroff -man | less

About the version with the graphical user interface

If you are using the Mac OS X version with the GUI (or you have compiled it up that way on Linux), after the program launches and reads the data, it opens up an information window and then it waits for you to hit the space bar to start the program running. At that point, if you have installed the NewHybrids_PreDefdViews.txt file as described below, you should be able to hit the "1" key on your keyboard and have a bunch of different windows open up to watch the progression of the MCMC.

Getting predefined view to work

Until I write a little installer package and change a few more things this is how you are going to have to manually install NewHybrids Predefined Views for OS X:

After cloning and building the repository you can move the file NewHybrids_PreDefdViews.txt to the directory ~/Library/gfmcmc,
creating the directory if it is not already there. In the above the ~ stands for your home directory.

Running a test data set

To see if you have it up and running on the test data set try issuing this command from the newhybrids directory:

./newhybs -d test_data/TestDat.txt

Then try hitting 1 key and then the space-bar.