ATGC Files

### ATGC1.0 README ###

### MANUAL ###

A Extensive manual is available in pdf format or using the application, in the 
option Tutorial of the main navigation bar.
ATGC is a open source application, for more information, new releases, download 
source code and complete virtual machines (see below) or download the manual please
visit the homepage: http://atgcinta.sourceforge.net
ATGC is available for installing in two ways, the first is a complete instalation 
mode (only tested for Linux machines) or the second is the use of virtual machines, 
downloading a VM image with the complete application (all requirements installed there).
For detailed installation instructions please view the INSTALL file.

### DESCRIPTION ###

ATGC is a web application that allows users to work with NGS transcriptomic 
data without a reference genome, using an ontology driven database schema to 
data store and management and provide interfaces to create schema structure 
and load ontologies and data, visualization, searching possibilities and data 
integration. Using this application is possible visualize, explore, analyze and 
share de novo transcriptomic data generated by NGS platforms using a Chado 
database to store the data. It is an open source and free available application, 
with support to store information in several Chado modules and uses different 
ontologies to classify data and then explore this data using a ontology structure 
with graphics, searches and description tables.
ATGC is open source, so all we ask is that you cite our paper in any publications 
that use this application:

    S. Gonzalez et. al. "ATGC Transcriptomics: A web-based application to integrate, explore and analyze de novo transcriptomic data"

### RUNNING APPLICATION (Using Web2Py executable) ###

The password is needed when the user want to access to the administrative interface
For the virtual machine mode installation replace <path to> by /home/atgc, for 
complete instalations replace by the correct path.

Using screen command:
    $ screen -S web2py
    $ <path to>/web2py.py --nogui

Using background:
    $ <path to>/web2py.py --nogui --password=password &

Using the graphical user interface (GUI):
    $ <path to>/web2py.py

Using machine as web server (with web2py http server, not with apache or other http server)
    $ screen -S web2py
    $ <path to>/web2py.py --nogui --interface='localhost:8000;<serverIP>:<port>'
In this way, other machines in the network can access to the application,
writing the following URL in a web browser: http://<serverIP>:<port>/ATGC/
The administrative interface is only accessible from the server machine.

### Application access using the web browser ###

To access to the application, write this URL in the web browser: http://localhost:8000/ATGC/

### CONTACT INFORMATION ###

Please address questions and bug reports to: gonzalez.sergio@inta.gob.ar

Last Revised July, 2016