Hi, is it possible to run HYPHY from the command line using the the Windows version 2.1.2?

I want to incorporate HYPHY into an external program, similarly to what MEGA5 appears to do, and therefore need to shell to it without launching the GUI.

Hi Michael,

If you have cygwin (or another Linux compatibility layer) installed on your Windows machine, you should be able to run HyPhy (and any other command line program) from it, after you compile it. Sorry there isn't a simpler solution at the moment.

Sergei

Thanks very much :), I will try that.

Hi Michael,

Good luck. Let me know if this works. You will want to get the latest HyPhy source code from Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login and then use CMAKE (a free tool that you may need to download separately) to compile HyPhy.

Sergei

Hi, so I managed to get the HYPHYMP target to compile (the Unix Cmake version, not the Windows) on Windows under cygwin, unfortunately I have a problem now with the paths that I can't seem fix:

[code]
C:\>C:\dev\test\hyphy\HYPHYMP.exe batch.bf
Error:
Could not read command file in ExecuteAFile.
Original path: 'C:/dev/test/hyphy/TemplateBatchFiles/PARRIS.bf'.
Expanded path: '/cygdrive/c/C//dev/test/hyphy/TemplateBatchFiles/PARRIS.bf'

Function call stack
1 : ExecuteAFile from file "C:/dev/test/hyphy/TemplateBatchFiles/PARRIS.bf" using basepath /cygdrive/c/.
reading input from inputRedirect
{"01":"Universal",
"02":"1",
"03":"C:/coding_finalout"}
-------
[/code]

The problem appears to be the basepath ("/c/cygdrive/" - probably because I have compiled under cygwin): it is prepended to the path I specify in my batch file (see Expanded path). Is there a way, preferably without modifying the source code, to change the basepath to be the empty string ""?

I want it to be able run on any Windows machine, so I don't want a fixed path. Thank you for your help.

Hi Michael,

You can specify BASEPATH=path and LIBPATH=path command line arguments that will replace the compile time default.
LIBPATH is where HyPhy will look for its Standard Analyses (i.e. the TemplateBatchFiles directory), while BASEPATH is the path prefix.

I have not tested this build however, so it may not work as expected. If the issue persists, let me know and I'll see what I can do to fix it.

Sergei