Changeset 180

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Timestamp:
03/25/09 11:19:22 (8 months ago)
Author:
cholt
Message:

update documentation

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  • INSTALL

    r174 r180  
    113113  a.  Unpack the Maker tar file into the directory of your choice (i.e. 
    114114      /usr/local). 
    115   b.  Now add the following to your .bash_profile if you haven't already: 
     115  b.  Change to the directory maker/perl and run Install.PL by typing: 
     116      perl Install.PL 
     117  c.  Now add the following to your .bash_profile if you haven't already: 
    116118        export WUBLASTFILTER="where_wublast_is/filter" 
    117119        export WUBLASTMAT="where_wublast_is/matrix" 
    118120        export ZOE="where_snap_is/Zoe" 
    119121        export AUGUSTUS_CONFIG_PATH="where_augustus_is/config" 
    120   c.  You can now run a test of Maker by following the instructions in the Maker 
     122  d.  You can now run a test of Maker by following the instructions in the Maker 
    121123      readme file. 
    122124 

  • README

    r174 r180  
    5454        MPI - contains MPI specific data to configure MAKER for a cluster that supports MPI. 
    5555        Apollo - contains gff3.tiers file (See section titled APOLLO below) 
    56         data  - contains some sample data used to make sure everything works 
     56        data - contains some sample data used to make sure everything works. 
     57        perl - contains perl modules that need to be compiled 
     58 
     59Finally change to the maker/perl directory and type: 'perl Install.PL' to compile required perl modules. 
     60 
     61Now you can run MAKER!! 
    5762 
    5863Maker uses control files to guide each run.  Generic control files can be built using the -CTL flag in maker.  These control files can then be edited by the user to identify the location of all required input data and statistics.  Control files are run specific and seperate control will need to be built for each genome given to maker.  Maker will look for control files in the current working directory, so it is recomended that maker should be ran in a seperate directory containing unique control files for each genome.