Environment: Linux 64 bits
The tools are tested on Ubuntu 16.04, 64bit.

1. Python and some packages

It is extremelly desirable that you work with python version 2.7.
Fortunately, the default version of python for Ubuntu 16.04 is 2.7, if you are using other Ubuntu release,
you might need the below instruction:
http://askubuntu.com/questions/101591/how-do-i-install-python-2-7-2-on-ubuntu

You might need to install the following dependencies before installing any python packages:
sudo apt-get install python2.7-dev libpng-dev libcurl3-dev

Execute the below command to install pip, which is a package management system used to install and manage software packages written in Python :
sudo apt install python-pip

Then, you can install python packages by command:
pip install --user setuptools wheel numpy scipy matplotlib cython

2. SRA toolkit (2.9.0)

Download the latest software at:
http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software

And place the binaries in any folder contained in your $PATH. Make sure they are executable (770).

3. Bedtools (2.25.0)

sudo apt install bedtools

4. Bowtie 2 (2.2.6)

To install Bowtie 2:
sudo apt install bowtie2

5. samtools (0.1.19)

To install samtools simply execute:
sudo apt install samtools

6. MACS (2.1.1.20160309)

pip install --user macs2

7. RGT (0.11.2)

First, you need to install the package MOODS, which cannot be automatically installed in our setup procedure:
pip install --user https://github.com/fabioticconi/MOODS/tarball/pypi-ready

To install RGT:
pip install --user RGT

You also need to download genome information for mouse genome mm10:
cd ~/rgtdata
python setupGenomicData.py --mm10

and setup the motif logo for HOCOMOCO repository:
python setupLogoData.py --hocomoco

9. IGV (2.4.9)

a) IGV needs Java (version 8), so if you don't have it install the JRE: http://askubuntu.com/questions/48468/how-do-i-install-java
b) Go to https://www.broadinstitute.org/igv/
c) Click in the download section
d) Search for "Binary Distribution". Download the binary distribution
e) Unzip the file and try to open IGV by executing the script "igv.sh"

f) If you are able to open IGV, you will see a dropdown menu in the up-right part of the IGV interface. This dropdown menu, 
just below the "File" menu, will contain the name of an organism (Human, Mouse, Baillus Subtillis or other)
g) Click on this menu and select "More..."
h) A window will appear. In the field "Filter" please type "mm10"
i) Select the item found, probably "Mouse mm10", click in the "download sequence" tick item and then in the "OK" button