Dear Greg,
I would suggest using (2) or (3). You can take a look at Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to
for an example of how to write wrapper files. If you want to use (3), you can try the following mechanism to pass arguments via a command line:
First, enumerate all the necessary options and generate their values.
Second, call (this works in sh and bash)
Code:$(echo option 1; echo option 2; .... echo last option) | mpirun -np xx /pathto/HYPHYMPI /pathto/HYPHY/TemplateBatchFiles/GARD.bf
replacing options X placeholders with actual values and using an appropriate MPI syntax for your install. Note that this trick only works if you can run interactive MPI jobs through the shell; if not try (2).
After the analysis is finished, run GARDProcessor.bf (standard analyses: recombination) on the output file generated by GARD.
Cheers,
Sergei