Orthologsorter
Version 2.0 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 Installation of required softwares and perl modules 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. Software: - Linux - MySQL Server $ sudo apt-get install mysql-server - Apache $ sudo apt-get install apache2 Perl Modules: - BioPerl $ sudo apt-get install bioperl - DBI libraries $ sudo perl -MCPAN -e "install DBI" Upload the fastas files To use Orthologsorter on your data, you need to collect protein fasta files ".faa" and put them in the directory "/projects//fastas". Configure Orthologsorter Some information used during execution of the program need to be set in the .cfg file. This file must be stored in the folder "/projects/". An example of this file may be seen in the folder "/doc". Running Orthologsorter The step by step to run orthologsorter is described in the user guide may be accessed in the folder "/doc". Orthologsorter Arguments myproject= Project name separated by "_". user= MySQL login provided by user. = The path of the cgi-bin directory of the local machine. = The path of the www directory of the local machine. School of Computing - Facom Federal University of Mato Grosso do Sul - UFMS Authors. Narielly Calista Farias, Nalvo Franco Almeida, nalvo@facom.ufms.br