Please see buildTools/BUILD.txt for build requirements and instructions. Note especially the section BUILD SPECIFIC MODULES. To build Analysis module, the command is: MODULES=Analysis ./buildTools/build.sh Tips: - If you are building this software for the first time, it's suggested to use a Docker container to build. That will reduce the chance of being blocked by any environment dependencies. https://hub.docker.com/r/iontorrent/tsbuild/ - Note that the code that was formerly in the ion-alignment and tmap packages is now rolled into the ion-analysis packages - For standalone Torrent Variant Caller, please see the below link for instructions. There are supported Docker containers for various platform. http://updates.iontorrent.com/tvc_standalone/README.txt https://hub.docker.com/r/iontorrent/tvcbuild/