INSTALL

GARLIC - An artificial non-functional realistic DNA sequence generator.

Copyright (C) 2011 Juan Caballero [Institute for Systems Biology]

INSTALLATION INSTRUCTIONS

All the code is in Perl, so basically just unpack/clone the package in a
convenient directory and add/create the models under data/

a) Unpacking a zip
   > unzip Garlic-master.zip

b) Clonning the repository from GitHub:
   > git clone https://github.com/caballero/Garlic.git
   
Note: the GIT repository only contains the code, no models are included.   
   
REPBASE DATA

The RepBase consensus sequences can be obtained from GIRI 
[http://www.girinst.org/server/RepBase/index.php], download and unpack the
EMBL format of RepBase.
  
  > cd data/RepBase
  > cp /path/to/RepeatMaskerLib_20090604.embl RepeatMaskerLib.embl
  
  where XXXX is the version number of RepBase.

createFakeSequence.pl looks for "RepeatMaskerLib.embl", please adjust the file
name if required in the code of createFakeSequence.pl.

OTHER

The scripts must work out-of-the-box, but minor changes might be required:

1. Perl path: the default is /usr/bin/perl, change it in all scripts if
   required.
2. Perl modules: we use standard modules: [Getopt, Pod, File, List], please
   use CPAN if your perl version doesn't include them.
3. Data dir: default is './data', you can modified this value as a parameter
   or changing the variable $data in the scripts.
4. createModel.pl require 'wget' and 'tar', you can adjust the path or change
   the commands in the source code.

TESTING

Run bin/test.sh to check if the installation works, it will model and create
and artificial sequence using the Fugu genome.