Put the libraries in their corresponding folder under /deps.
I will not go through the process of setting up Emscripten, if you have any troubles check out their excellent wiki or mailling list.
Boost does not need to be build, just put the sources in the corresponding folder.
Run the following command in /deps/snappy-1.1.1:
emconfigure ./configure
emmake make
See the README.md in /deps/protobuf-2.5.0/ on how to build Protobuf.
Run the following commands:
mkdir build && cd build
CC=emcc CXX=em++ cmake .. -DBUILD_EMSCRIPTEN=1 -DBUILD_ADDON=1 -DBUILD_EXAMPLE=1
make
This will generate the examples and the Alice library as LLVM-Bytecode.
Thought the examples compile, you will get an error about being unable to load the replay when you try to run them. This happens Emscripten's File I/O abstration library is not automatically embedded in the generated Javascript.
In order to run the examples you will have to edit the html generated to include the Filesystem Api. There are some examples on the Emscripten Wiki.