The gro bacterial micro-colony growth specification and simulation software.
The latest documentation for gro is available from
http://depts.washington.edu/soslab/gro/docview.html
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
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 rungro
from thexterm
window.
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
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