murrayrm / gro

The gro bacterial micro-colony growth specification and simulation software. For more information see the gro website, listed below.

gro

The gro bacterial micro-colony growth specification and simulation software.

Documentation

The latest documentation for gro is available from

http://depts.washington.edu/soslab/gro/docview.html

Compiling

MacOS

You will need the following packages in order to compile gro:

• CCL: https://github.com/klavinslab/ccl
• Chipmunk 5.3.5: https://chipmunk-physics.net/release/Chipmunk-5.x/
• XCode

Once you have these pre-requisties, you can install gro by running qmake and telling it where to find the ccl and chipmunk source directories (which should also have the compiled library files).

qmake CCL=<cclpath> CHIPMUNK=<chipmunkpath>
make

This will create directory gro.app that can run using the command

open gro.app

Linux

You will need the following packages in order to compile gro:

• CCL: https://github.com/klavinslab/ccl
• Chipmunk 5.3.5: https://chipmunk-physics.net/release/Chipmunk-5.x/
• Linux build tools (via apt): build-essential, flex, bison, libreadline-dev
• OpenGL: freeglut3-dev

Once you have these pre-requisties, you can install gro by running qmake and telling it where to find the ccl and chipmunk source directories (which should also have the compiled library files).

qmake CCL=<cclpath> CHIPMUNK=<chipmunkpath>
make

The file useful/chipmunk.gro in the main gro directory is available to allow compilation of chipmunk via qmake. To use it, copy useful/chipmunk.gro to the chipmunk main source directory and run qmake then make.

If you are running gro on a remote host and you are using X11 fowarding back mac to a Mac, please note the following:

• Run ssh -Y (not -X) to forward the X11 connection

• If you have font rendering problems, try running xterm and then run gro from the xterm window.

Windows

Running gro

The gro application should open a window from which you can load and run gro programs. The following environment variables can be used to help gro find files that it needs:

GROHOME	Initial directory for opening `gro` files
GROPATH	Colon-separate list of directories to search for include files

Apple Paths

If you are on a Mac you may have discovered an issue with gro not starting properly because of an old directory structure issue. David Soloviechik uses this AppleScript to solve that problem

tell application "Finder"
	set current_path to container of (path to me) as alias
end tell
set dir to (POSIX path of current_path)
do shell script "cd \"" & dir & "\" && gro.app/Contents/MacOS/gro > /dev/null 2>&1 &"

To use this script, put it in a file called run_gro.scpt within the gro directory and then at the command line run

> osascript run_gro.scpt