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1.3 Get and set up the examples

This tutorial assumes that someone else has already installed the MORGAN software somewhere. If not, please contact your local system administrator or download the software yourself and follow the instructions therein. Overview of MORGAN.

Follow the following steps to download and set up the examples:

  1. Download the examples (gzipped tar files): morgan-examples.tar.gz

  2. Unpack the examples by typing the following command in a shell window,

     
    user$ tar zxvf morgan-examples.tar.gz
    

    Or if the above command fails (you don't have GNU tar), use

     
    user$ gunzip -c morgan-examples.tar.gz | tar xvf -
    

    This will produce a `morgan-examples' directory under your current directory.

  3. You need to edit the `Makefile' (using your favorite text editor, for instance vi or pico) in the `morgan-examples' directory to make sure the paths to your MORGAN programs are correct.

    Here is the relevant part of the `Makefile',

     
    # Change the following macros to where MORGAN is installed on your 
    # system!!!
    
    MORGANDIR = /castor/genepi/MORGAN_V2.6
    
    # ===== Usually not necessary to edit these ======
    
    LMAUTO = $(MORGANDIR)/Autozyg/lm_auto
    LMPVAL = $(MORGANDIR)/Autozyg/lm_pval
    LMLODS = $(MORGANDIR)/Autozyg/lm_lods
    LMBAYE = $(MORGANDIR)/Autozyg/lm_bayes
    LMMRKS = $(MORGANDIR)/Autozyg/lm_markers
    
    PEDCHK = $(MORGANDIR)/PedComp/pedcheck
    KIN    = $(MORGANDIR)/PedComp/kin
    
    GENDRP = $(MORGANDIR)/Genedrop/genedrop
    IBDDRP = $(MORGANDIR)/Genedrop/ibddrop
    
    MULVAR = $(MORGANDIR)/PolyEM/multivar
    
    RM = rm -f
    
    # ===== No editing necessary below. ======
    

    Change MORGANDIR to the base directory of MORGAN installed on your system. Ordinarily this is the only change one needs to make to run the tutorials.

    By default, the compiled executable programs are in various subdirectories of the base directory. Programs can be run using make or gmake. You may type:
     
    make help
    
    to see instructions on how to do this. Alternately type:
     
    make links   (on Linux)
    make linka   (on Unix)
    
    to make symbolic links to those programs in the current directory and then you can call them directly as in the tutorial.

Notes for Microsoft Windows users:

Windows users should download the examples and download and install Morgan 2.6 the usual way. Then, move the executable programs to the examples directory.

Please note that MORGAN programs are command-line based tools, meaning that there is no icon to click and you need to make yourself comfortable with working in the "Command Window" (called up by pressing the Windows key and R together, typing in cmd and then pressing return).

`Makefile' is not as useful under Windows. However, if you put the programs into the same directory as the examples, you can run the programs directly by typing the corresponding commands in the examples directory.


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