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Running a program in Linux and macOS

Command line software

BLUPF90 programs are command-line software. Each program reads a parameter file describing the names of the data and pedigree files, the model, and the covariance components used in the analysis. It displays logs on the screen and writes one or more output files. These programs are designed to be used in a shell environment with keyboard input.

Here, we assume a standard bash environment. For macOS, all operations will be performed in Terminal. No graphical user interface (GUI) is used.

Note: Currently, only Intel-based Macs are supported. The recent Macs with Apple M-series (ARM-based) CPUs are not supported.

Installation

No special installation procedure is required. Just download the program from the official website. Then, change the file permissions using chmod, for example, chmod 755 or chmod u+x (a helpful way to remember: ch_ange the mod_e to add execution permission +x for the _u_ser). You can move the program to your preferred directory, which may already be listed in your PATH environment variable. If not, you can create such a directory and move the program there.

Here is an example:

# 1. Download the program. You can also use curl or another method.
wget http://nce.ads.uga.edu/html/projects/programs/Mac_OSX/new/blupf90

# 2. Change the permission to make it executable.
chmod 755 blupf90

# 3. Create a directory for binaries, if it doesn't exist.
mkdir ~/bin

# 4. Move the program to that directory.
mv blupf90 ~/bin

You can use other tools such as curl instead of wget to download the file. If the directory (e.g., ~/bin) is not listed in your PATH environment variable, you need to add it. Check the current PATH using:

echo $PATH

If your directory is listed, you’re all set. If not, add it by typing:

export PATH=~/bin:$PATH

If the program is located in a different directory, replace ~/bin with the correct path. This setting is temporary and will disappear when you log out. To make it permanent, add the command to your .bash_profile. If you’re unsure how to do this, open .bash_profile with a text editor and add the line to the end. Log out and log back in for the change to take effect.

Running a program

Navigate to the directory that contains all the required files (e.g., pedigree, data). Then, type the program name to start it. If the program launches successfully, you will see a message like:

name of parameter file?

At this prompt, type the name of the parameter file. Some programs, especially Gibbs sampling ones, will require additional inputs. The messages will appear on screen (standard output), and you can save them to a file using redirection:

# Save all messages to a file.
# The program still accepts input even if nothing is shown.
blupf90 > out.txt

# Save messages to a file while also displaying them on screen.
blupf90 | tee out.txt

You can also avoid manual input at the start of the program:

# Provide the parameter file name via echo.
echo parameter.txt | blupf90

# Or use a file.
echo parameter.txt > input
blupf90 < input

The second method is especially useful for Gibbs sampling programs that require several lines of input.

Stop a program

To stop the program immediately, press Ctrl + C. For convenience, you can hold down Ctrl and tap C. The program will terminate immediately, and any resulting messages can be safely ignored. In some cases, especially during multi-threaded computations, the program may continue running after receiving the stop signal. If that happens, simply close the terminal window to stop the program completely.

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