Dear Albert,

All of your suggestions are excellent!

Quote:


You can do this to an extent. The steps are as follows (assumes a GUI version)

(1). Set up your analysis normally; i.e. Build Likelihood Function but do not Optimize. Click on the little gearwheel button in the console window
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to call 'ExportLikelihoodFunction'. When prompted, choose to include the optimize command. This sequence will save a self contained analysis (data, models, tree etc) into a HyPhy batch file.  You can then load this analysis into a GUI or command line version of HyPhy and run the optimization.

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If you saved your file to file named 'myFile.bf' you can then call

$HYPHY BASEPATH=path to hyphy myFile.bf -p

Note the -p flag to allow you to invoke result processing modules after the analysis is done (this assumes an interactive run).

Quote:


This is an excellent idea, but currently there is no way to do this generally (for different data/tree/model options) - although this feature IS on my list of things to do...

You might have to write your own batch file or modify an existing one to write a 'Template' analysis (much like the standard analyses in HyPhy are done). If there is anything in particular you want to do, I'll be happy to help you get started.

HTH,
Sergei

Dear Albert,

Quote:


If you build a command line version of HyPhy you can always write all the relevant inputs into a text file (one on each line) and then pipe it to HyPhy as in (assuming you are in the HyPhy directory):

$HYPHY  TemplateBatchFiles/TestBranchDNDS.bf < myInFile > myOutFile &

A more tedious way to do this is to make a copy of the batch file you want to pre-define the input for and replace commands:

fscanf (stdin, something, something);

with

fscanf ("myConfigFile", something, something);

where "myConfigFile" contains the input you want to feed the analysis (one entry per line).


HTH,
Sergei