The sh file is the installer for MEGAN.
You first have to run the installer to install the program.
To run the installer in command-line mode, type
./MEGAN_Community_unix_6_18_10.sh -c
The option -c stands for “console mode”.
Once installed, you can find MEGAN command line programs in the megan/tools directory.
The community edition of MEGAN doesn’t have a command-line option.