eFORGE is the epigenetic equivalent of the FORGE tool. For details of the FORGE analysis approach see documentation in the FORGE web version at
 
http://www.1000genomes.org/forge-analysis

eFORGE is also available as a web tool at 

http://eforge.cs.ucl.ac.uk/

1. The script itself is currently called eforge.pl written in Perl. It has
the following Perl dependencies.

use 5.012;

use warnings;

use DBI;

use Sort::Naturally;

use Cwd;

use Storable;

use Getopt::Long;

2. The sqlite3 db file that stores the bitstrings. This file is called eforge_1.1.db currently.

3. A stored hash containing the parameters for the background selection.
Currently two files, one with the 27k and one with the 450k annotation data (mvp_bins).

The database and the hashes are downloadable from:
http://eforge.cs.ucl.ac.uk/?download

4. An eforge.ini file in the same directory as the script. Edit this to provide the
directory in which the database and hash are stored.

5. An R 3.0 installation with the "devtools" and "rCharts" packages installed. See

https://github.com/ramnathv/rCharts. You will need to install the latest version e.g.

require(devtools)
install_github('rCharts', 'ramnathv', ref = "dev")

The input data is one of several options.

a. A list of 450k probeids (DMPs)

b. BED format (for 450k probes)

The analysis requires a minimum of 5 DMPs (this is not a strict limit but
operationally is best).

To work DMPs currently have to be on either the 27k or the the 450k array. The
script gives warnings on DMPs not found.

It also warns for background sets that do not have the right number of probes
chosen, but this is really for information only.

It takes a series of command line options as follows

-f : the file to run on

-data : whether to analyse ENCODE (encode) or Epigenome Roadmap (erc) data

-label : a name for the files that are generated and for the plot titles
       where there is a title.

-format : for the input data format. If this is location data e.g.
         bed format, the probeid is obtained from
         the sqlite3 database.
 
Some of these default as described in the perldoc. Minimally the command
line is:

eforge.pl -f probeidfile -label Some_label

which will by default run on Epigenome Roadmap data

OUTPUT
======
there are several outputs generated

1. A pdf static chart, that would be good for download.

2. A d3 interactive chart.

3. A Datatables table.

4. R code files for generating the charts and the table.

5. There is also a tsv file of the results.

WEBSERVER
=========

To install the web interface, please refer to the INSTALL document in the webserver folder.