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

iBrowser can be downloaded as an self contained (Virtual Box) virtual machine using BitTorrent Sync and this read-only key: key (860Mb).

A manual can be found here

The data used in the iBrowser paper can be downloaded using BitTorrent Sync using the following read-only key: key.

The data consists of:

total 39G
9.1G arabidopsis_50k.sqlite
1.5K arabidopsis_50k.sqlite.nfo
6.4G RIL_10k.sqlite
1.5K RIL_10k.sqlite.nfo
1.5K RIL_50k_mode_ril_delete_greedy.sqlite.nfo
1.6G RIL_50k_mode_ril_delete.sqlite
1.5K RIL_50k_mode_ril_delete.sqlite.nfo
995M RIL_50k_mode_ril_greedy.sqlite
1.5K RIL_50k_mode_ril_greedy.sqlite.nfo
1.6G RIL_50k_mode_ril.sqlite
1.5K RIL_50k_mode_ril.sqlite.nfo
1.6G RIL_50k.sqlite
1.5K RIL_50k.sqlite.nfo
1.5K RIL.customorder
 67M tom84_10k_introgression.sqlite
1.5K tom84_10k_introgression.sqlite.nfo
 11G tom84_10k.sqlite
1.5K tom84_10k.sqlite.nfo
 27M tom84_50k_introgression.sqlite
1.5K tom84_50k_introgression.sqlite.nfo
3.1G tom84_50k.sqlite
1.5K tom84_50k.sqlite.nfo
3.0K tom84.customorder
3.9G tom84_genes.sqlite
1.5K tom84_genes.sqlite.nfo

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

for standalone:

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 [email protected]:sauloal/introgressionbrowser.git

cd introgressionbrowser

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

Open your browser at 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

The virtual machine should login automatically.

The only procedure necessary is to share your data folder (in your host computer) as "DATA". A step-by-step manual can be found here.

After booting your virtual machine: To Start:

./start.sh

To Stop press Ctrl+C: To shut down type:

off

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

In case you want/need to do it manually, please find bellow instructions:

wget http://download.virtualbox.org/virtualbox/4.3.6/VBoxGuestAdditions_4.3.6.iso
mkdir vbox
mount VBoxGuestAdditions_4.3.6.iso vbox
cd vbox
./VBoxLinuxAdditions.run
cd ..
umount vbox
edit /etc/fstab adding
  data /media/data vboxsf re 0 0
mount -a
ls /media/data

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

mkdir /mnt/cdrom
mount /dev/cdrom /mnt/cdrom
mkdir ~/vm
cd ~/vm
tar xvf /dev/cdrom/VMwareTools-9.6.1-1378637.tar.gz
cd vmware-tools-distrib
./vmware-install.pl -d
cd ../..
rm -rf vm
ls /mnt/hgfs/data

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)