GDV is a fast and easy to use genome browser. The main goal is to provide a tool for biologist and bioanalysts who wants to VISUALIZE and ANALYSE their data in an interactive and responding way.

A production version is running on bbcf. You can log in if you have an account on tequila which is automatic if you have a university account in Switzerland. If not, we will provide soon a demo version available for everybody. If you really wan't to test GDV, please sent a email to bbcf webmaster.

pyGDV is written in python, so the recommended way of installing it (as all python modules) is throught a virtual environment. Here we put notes on installing virtualenv (will build your virtual environment) & virtualenvwrapper (will make it easier to work with virtualenv).

Please refers to the official documentation if something goes wrong.

1. Install devellopers packages (already done usually).

   • Xcode (MacOS)
   • python-dev & build-essential (Debian, Ubuntu)
   • python-devel (Fedor)

2. Install virtualenv sudo easy_install virtualenv

1. Install python pip (package manager)

2. Install vitualenvwrapper: pip install virtualenvwrapper

3. Define the directory that will contains your environements export WORKON_HOME=/usr/local/env (add in .bashrc) mkdir $WORKON_HOME

4. Execute virtualenwrapper.sh then source it source /usr/local/bin/virtualenvwrapper.sh (add in .bashrc)

5. Create the virtual environement that will contains GDV mkvirtualenv --no-site-packages -p python2.6 pygdv

You can now enter the virtual env with workon pygdv and exit with deactivate

It's not mandatory to install pyGDV on a virtualenv but it's recommended.

-- DRAFT --

1. Install git (do it throught your package manager)

2. Go to the directory where you want to install pyGDV.

3. Execute :

       git clone https://github.com/yjarosz/pygdv
       cd pygdv
       python setup.py install
       easy_install celery
       easy_install webob==1.1.1
       easy_install numpy
       easy_install matplotlib
       pip install -U kombu-sqlalchemy
   

4. Install bbcflibs clone libraries bbcflib (git), bein (git), track (git), gMiner (git) a script will soon be provided to install them at once

5. Add them to the virtualenv

    add2virtualenv bbcflib
    	add2virtualenv track
    	add2virtualenv bein
    	add2virtualenv gMiner
   

6. copy developement ini file to make it for production cp development.ini production.ini

7. enter info needed in production.ini

8. cp who.ini.sample who.ini

9. fill who.ini

10. paster setup-app production.ini

11. prefix your application if needed

12. enter the ip of the proxy if needed

13. run ``paster serve production.ini`

14. configure worker in celeryconfig.py

15. run workers : celeryd

Useful startup scripts are pygdv_ctl& celery_ctl. You should look at them.

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