Use the hello-stk example to get started.
$ mkdir javacard
$ cd javacard
$ git clone https://github.com/Shadytel/sim-tools.git
$ git clone https://github.com/Shadytel/hello-stk.git
$ cd hello-stk
$ make
To install the applet onto a SIM card, first set the type of reader you are using.
# For PCSC readers:
$ export SHADYSIM_OPTIONS="--pcsc"
# For USB-serial readers:
$ export SHADYSIM_OPTIONS="--serialport /dev/ttyUSB0"
$ make install
The shadysim tool has lots of other options.
$ ./sim-tools/bin/shadysim --help