Managed to create a comparison file for two RMA6 MEGAN files using the command-line as follows:
$ /Applications/MEGAN_Ultimate-Edition/MEGAN.app/Contents/MacOS/JavaApplicationStub -g -E < CompareSamples.txt
where CompareSamples.txt contains the following commands:
compare mode=RELATIVE meganfile=’/path/to/file1.rma6’ ‘/path/to/file2.rma6’;
save file=’/path/to/comparing-two-files.megan’
quit;
Now, the question would be whether there’s a more elegant/optimum way to specify a large number of file names in the “compare” command, specifically in the meganfile= parameter. Right now I can only think to add the names individually to my CompareSamples.txt file. A more optimum way could be something like reading a list from a file or opening all RMA6 files in a specific directory. Not sure if MEGAN command line supports this kind of interactions?
Any thoughts regarding this?
Thank you very much 
