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 Login 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

Dear Greg,

Good point about an MPI environment error, I forgot about that.
The GARD sequence is as follows:

• Which alignment to screen? (path)
• Which nucleotide biases to use? (e.g. 010010 - a 6 char string)
• Rate variation: select from (case sensitive)
  
  • None - Homogeneous rates across sites (fastest)
  • General Discrete - General discrete distribution on N-bins
  • Beta-Gamma - Adaptively discretized gamma N-bins. Try is GDD doesn't converge well, or if you suspect a lot of rate classes and do not want to overparameterize the model
• If other than None chosen above, enter the number of rate classes (a number in 2-32 range)
• Where to save the results? (path)

Cheers,
Sergei