Installation

• Get Data
• Interface
• Installation
  • Docker
  • Virtual Machine
    • VirtualBox
    • VMWare
  • Manually
    • Getting the code
    • Global dependencies
      • Visualization
        • Standalone
          • Install Linux dependencies
          • Install Python dependencies
        • Apache
          • Install Apache dependencies
      • Calculations

Get Data

The data used in the iBrowser paper can be found HERE

Interface

The Web User Interface (Web UI) works in Chrome 37+ and Firefox 33+. The UI behaviour in iExplorer is erratic and therefore we discourage the use of this web browser. We haven't tested Opera and Safari web browsers, feedback is welcome.

click to enlarge

Installation

Docker

You will need to run docker once to create the config file, edit it and then run again

for standalone, run:

docker run -it --rm \
-v $PWD/data:/var/www/ibrowser/data \
-p 127.0.0.1:10000:10000 \
--name ibrowser \
sauloal/introgressionbrowser ./ibrowser.py data/

for local copy, run:

git clone git@github.com:sauloal/introgressionbrowser.git

cd introgressionbrowser

docker run -it --rm \
-v $PWD:/var/www/ibrowser2/ \
-w /var/www/ibrowser2 \
-p 127.0.0.1:10000:10000 \
--name ibrowser sauloal/introgressionbrowser \
./ibrowser.py data/

please notice that data should be added in introgressionbrowser/data

please notice that, for security reasons, iBrowser is only available to the local computer. To change that or to run inside Docker, please edit data/config.py:

SERVER_IP      = '0.0.0.0'

If you are not allowed to edit data/config.py,

docker run -it --rm \
-v $PWD:/var/www/ibrowser2/ \
-w /var/www/ibrowser2 \
-p 127.0.0.1:10000:10000 \
--name ibrowser \
sauloal/introgressionbrowser \
chown $(id -u):$(id -u) data/config.py

Open your browser at http://127.0.0.1:10000

Replace 127.0.0.1 for 0.0.0.0 in the command line if you want others in your network to be able to access your iBrowser instance.

Replace the -it for -d to run in the background

Virtual Machine

VirtualBox

iBrowser can be downloaded as an self contained (Virtual Box) virtual machine from HERE.

The only procedure necessary is to share the folder in your computer containing the processed data as "DATA". The procedure is described in the step-by-step manual found HERE.

The virtual machine will login automatically.

After booting your virtual machine:

To start iBrowser:

./start.sh

To Stop iBrowser: press Ctrl+C:

To shut down the virtual machine: type

off

NEVER PUT THE MACHINE TO SLEEP OR CLOSE IT WITHOUT PROPERLY SHUTTING IT DOWN

VMWare

currently there's a bug in vmware which doesn't allows for the mounting of shared folders. For this reason vmware is not currently supported

Manually

Getting the code

Clone or download Introgression Browser.

git clone https://github.com/sauloal/introgressionbrowser

Global dependencies

Global dependencies - Visualization

Global dependencies - Visualization - Standalone

Install Linux dependencies

apt-get install -y -f build-essential checkinstall openssl sqlite3 libsqlite3-dev               \
                      libfreetype6 libfreetype6-dev zlib1g-dev libjpeg62 libjpeg62-dev          \
                      pkg-config libblas-dev liblapack-dev gfortran zlib1g-dev

apt-get install -y -f python-setuptools python-dev python-numpy python-scipy                    \
                      python-matplotlib python-pandas python-sympy python-pip python-imaging    \
                      python-numpy

Install python dependencies

pip install --requirement requirements.txt

OR

easy_install --user flask
easy_install --user ete2
easy_install --user sqlalchemy
easy_install --user Flask-SQLAlchemy
easy_install --user pysha3
easy_install --user pycrypto

If not possible to install python libraries system wide with apt-get, install also:

easy_install --user Pillow
easy_install --user Image
easy_install --user numpy
easy_install --user scipy
easy_install --user matplotlib
easy_install --user MySQL-python

Global dependencies - Visualization - Apache

Besides all standalone dependencies.

Install Apache dependencies

apt-get install -y -f libapache2-mod-wsgi apache2 

Global dependencies - Calculations

• Besides all standalone dependencies. *

Install pypy (Optional, but speeds up analysis)