I want to be able to call cisTEM commands from the command line without using interactive mode.
I know you can call the binaries like $ ./refine3d from a terminal and get an interactive session. But this is not conducive to scripting, since the arguments have to be passed in individually.
I think this must be possible because the way the GUI calls commands (from "Run Profiles") appears to be by issuing some bash command. However, the contents of $command is not useful in trying to run jobs independently, it contains some IP addresses and a number.
In the source code, "userinput.cpp" appears to have support for a "scripted mode", based on whether the caller is a tty. However, I am not sure whether this is implemented.