The following is a strawman setup of a two-layer MuPix-XY based detector for potential muSR applications. It is based on the mu3e software.
Basic setup on merlin-l-001
Log in to merlin-l-001 with your username USER and install a mu3e developer environment (using ursl's forked bitbucket repo). The following is based on tcsh, you'll have to translate for bash or other versions. 
The initial part of the above procedure needs to be done once. Note that the sourcing of setup.csh will induce dependencies on langenegger's  (!) privately compiled GEANT version (the official mu3e software on merlin is not yet in that state because of the Qt dependency). It also changes your settings (in case they exist) for gcc, boost, git, cmake, Qt, ROOT, and eigen.
How to run
Running the GEANT4 geometry display
cd /data/user/$USER/mu3e-musrSim source setup.cshcd run
mkdir data  #or link to somewhere 
../_build/mu3eVis
Running mu3eSim to show the GEANT trajectories
cd /data/user/$USER/mu3e-musrSim source setup.cshcd run
../_build/mu3eSim --gui
 
 
