Install and run Augustus on CentOS

Hello Folks .. If you are visiting this blog you definitely know what Augustus is all about, but still for any exceptions, here’s its short introduction taken directly from its makers:

“Augustus is an open source system for building and scoring statistical models designed to work with data sets that are too large to fit into memory“

Although the Augustus documentation is an elaborate and wonderful source of guidelines and information, this blog presents a crisp and condensed bunch of steps you can use to install Augustus and try one of the examples. So open a terminal on your machine and try the following steps:

Step 1. Python 2.6 needs to be installed on the machine as a prerequisite. If already installed, check the version of your python by typing the command "python" on the terminal. If it is 2.6, the output should be:

Python 2.6.6 (r266:84292, Jun 18 2012, 14:18:47) [GCC 4.4.6 20110731 (Red Hat 4.4.6-3)] on linux2 Type "help", "copyright", "credits" or "license" for more information.                                          >>>

Step 2. Run

sudo rpm -Uvh http://dl.fedoraproject.org/pub/epel/5/x86_64/epel-release-5-4.noarch.rpm

Step 3. Run 

sudo yum install numpy

Step 4. Enter the python shell and import

> python2.6 Python 2.6.6 (r266:84292, Jun 18 2012, 14:18:47) [GCC 4.4.6 20110731 (Red Hat 4.4.6-3)] on linux2 Type "help", "copyright", "credits" or "license" for more information.                                          >>> import numpy >>> numpy.__version__ '1.4.1' >>>

Step 5. Execute

mkdir AUGUSTUS_INSTALLATION

Step 6. Execute

wget http://augustus.googlecode.com/files/Augustus-0.4.4.0.tar.gz

Step 7. Execute 

tar -xzvf Augustus-0.4.4.0.tar.gz

Step 8. Execute

cd Augustus-0.4.4.0 (check that the setup has a "bin" folder containing files like "AugustusPMMLConsumer")

Step 9. Run

sudo python2.6 setup.py install

Last segment of the command output should resemble:

byte-compiling /usr/lib/python2.6/site-packages/augustus/modellib/baseline/tools/__init__.py to __init__.pyc byte-compiling /usr/lib/python2.6/site-packages/augustus/modellib/baseline/tools/userInitializeModels.py to userInitializeModels.pyc byte-compiling /usr/lib/python2.6/site-packages/augustus/modellib/baseline/tools/xml_fifo_io2.py to xml_fifo_io2.pyc byte-compiling /usr/lib/python2.6/site-packages/augustus/modellib/baseline/tools/fake_score_handler.py to fake_score_handler.pyc byte-compiling /usr/lib/python2.6/site-packages/augustus/modellib/baseline/tools/userMySQLInterface.py to userMySQLInterface.pyc byte-compiling /usr/lib/python2.6/site-packages/augustus/modellib/clustering/__init__.py to __init__.pyc byte-compiling /usr/lib/python2.6/site-packages/augustus/modellib/clustering/producer/Producer.py to Producer.pyc byte-compiling /usr/lib/python2.6/site-packages/augustus/modellib/clustering/producer/__init__.py to __init__.pyc byte-compiling /usr/lib/python2.6/site-packages/augustus/modellib/tree/__init__.py to __init__.pyc byte-compiling /usr/lib/python2.6/site-packages/augustus/modellib/tree/producer/Producer.py to Producer.pyc byte-compiling /usr/lib/python2.6/site-packages/augustus/modellib/tree/producer/__init__.py to __init__.pyc running install_scripts copying build/scripts-2.6/__setpath.py -> /usr/bin copying build/scripts-2.6/userInitializeConfigs -> /usr/bin copying build/scripts-2.6/realpmml -> /usr/bin copying build/scripts-2.6/unitable -> /usr/bin copying build/scripts-2.6/AugustusBaselineProducer -> /usr/bin copying build/scripts-2.6/fake_event_source -> /usr/bin copying build/scripts-2.6/AugustusClusteringProducer -> /usr/bin copying build/scripts-2.6/runfifo -> /usr/bin copying build/scripts-2.6/AugustusTreeProducer -> /usr/bin copying build/scripts-2.6/munge -> /usr/bin copying build/scripts-2.6/fake_score_handler -> /usr/bin copying build/scripts-2.6/userInitializeModels -> /usr/bin copying build/scripts-2.6/AugustusPMMLConsumer -> /usr/bin copying build/scripts-2.6/AugustusNaiveBayesProducer -> /usr/bin copying build/scripts-2.6/userBuildMySQL -> /usr/bin changing mode of /usr/bin/__setpath.py to 755 changing mode of /usr/bin/userInitializeConfigs to 755 changing mode of /usr/bin/realpmml to 755 changing mode of /usr/bin/unitable to 755 changing mode of /usr/bin/AugustusBaselineProducer to 755 changing mode of /usr/bin/fake_event_source to 755 changing mode of /usr/bin/AugustusClusteringProducer to 755 changing mode of /usr/bin/runfifo to 755 changing mode of /usr/bin/AugustusTreeProducer to 755 changing mode of /usr/bin/munge to 755 changing mode of /usr/bin/fake_score_handler to 755 changing mode of /usr/bin/userInitializeModels to 755 changing mode of /usr/bin/AugustusPMMLConsumer to 755 changing mode of /usr/bin/AugustusNaiveBayesProducer to 755 changing mode of /usr/bin/userBuildMySQL to 755 running install_egg_info Writing /usr/lib/python2.6/site-packages/Augustus-0.4.4.0-py2.6.egg-info

Step 10. Running

python2.6

should return

Python 2.6.5 (r265:79063, Apr 9 2010, 11:16:46) [GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2 Type "help", "copyright", "credits" or "license" for more information.                                          >>> import augustus.const as AUGUSTUS_CONST >>> AUGUSTUS_CONST._AUGUSTUS_VER ’0.4.2.0’ >>>

Installation is complete.

Step 11. To run an example:

> cd AUGUSTUS_INSTALLATION/Augustus-0.4.4.0/examples/basic                                      > python2.6 top-ten.py ../auto/data/training.nab

Sample O/P:

Field: Date       ( 5.38500%) '2000-12-14'       ( 5.27600%) '2000-12-29'       ( 5.10800%) '2000-12-22'       ( 5.04100%) '2000-12-18'       ( 4.99900%) '2000-12-04'       ( 4.90000%) '2000-12-07'       ( 4.83400%) '2000-12-03'       ( 4.76000%) '2000-12-05'       ( 4.71900%) '2000-12-11'       ( 4.56300%) '2000-12-26' Field: Color       (28.86200%) 'Black'       (24.45700%) 'Blue'       (23.75900%) 'Green'       (22.92200%) 'Red' Field: Automaker       (21.98000%) 'Mazda'       (21.35700%) 'BMW'       (19.88900%) 'Toyota'       (18.56900%) 'Volvo'       (18.20500%) 'Audi'

That’s it.  Hope it helped.