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<b>Orthologsorter</b><br>Version 2.0
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Before orthologsorter can be used, some requirements need to be
installed, as described in the UserGuide.txt file.  All programs
except MySQL Server, Apache and Perl are provided as part of the
Orthologsorter download.  The user guide may be accessed in the folder
"/doc".

Preconditions: A Linux System, MySQL Server, Apache, Perl and some
experience with Linux & Perl

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<b>Installation of required softwares and perl modules</b>
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Orthologsorter is automatic pipeline which aims to compare and analyze
bacterial genomes. This pipeline requires some softwares and perl modules
to run, as listed below. The installation example cited is for Ubuntu.

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Software:       
- Linux
- MySQL Server
    $ sudo apt-get install mysql-server
- Apache
    $ sudo apt-get install apache2

Perl Modules:
- BioPerl
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    $ sudo apt-get install bioperl
- DBI libraries
    $ sudo perl -MCPAN -e "install DBI"
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<b>Upload the fastas files</b>
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To use Orthologsorter on your data, you need to collect protein fasta
files ".faa" and put them in the directory "/projects/<myproject>/fastas".

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<b>Configure Orthologsorter</b>
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Some information used during execution of the program need to be set
in the <myproject>.cfg file. This file must be stored in the folder
"/projects/<myproject>". An example of this file may be seen in the folder
"/doc".

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<b>Running Orthologsorter</b>
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The step by step to run orthologsorter is described in the user guide
may be accessed in the folder "/doc".

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<b>Orthologsorter Arguments</b>
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 myproject=<String>                     Project name separated by "_".
 user=<String>                          MySQL login provided by user.
 <path/cgi-bin>=<String>                The path of the cgi-bin directory
                                        of the local machine.
 <path/var/ww/>=<String>                The path of the www directory
                                        of the local machine.

School of Computing - Facom
Federal University of Mato Grosso do Sul - UFMS
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Authors. Narielly Calista Farias, Nalvo Franco Almeida, nalvo@facom.ufms.br