Minor issue:
calcAlignedAsigs.py takes an argument called --signalSubfolder, which points to where the signal block has been generated. This block was generated by assembleExperimentData.py, which uses the argument --analysisName to determine where to save the block. Since these arguments are named differently docopt cries foul if the same shell script variable (say $ANALYSISFOLDER) is used for both, which causes calcAlignedAsigs.py to print its usage and quit.
Minor issue:
calcAlignedAsigs.pytakes an argument called--signalSubfolder, which points to where the signal block has been generated. This block was generated byassembleExperimentData.py, which uses the argument--analysisNameto determine where to save the block. Since these arguments are named differentlydocoptcries foul if the same shell script variable (say$ANALYSISFOLDER) is used for both, which causescalcAlignedAsigs.pyto print its usage and quit.