INSTALL

Installing prerequisites as packages is tested only for 
Ubuntu 12.04+ and other debian-derived systems


1. Installing TurboGears

TurboGears is meant to run inside python virtualenv and provides its own private index
to avoid messing with your system packages and to provide a reliable set of packages that will correctly work together.
Be sure that you are in virtualenv mode during all installation procedure.
$ sudo apt-get install python
$ sudo apt-get install python-virtualenv
$ virtualenv tg2env
$ tg2env/bin/pip install tg.devtools
$ source tg2env/bin/activate
(tg2env)$ #now you are ready to work with TurboGears

Start the project:

(tg2env)$ gearbox quickstart molgears
(tg2env)$ cd molgears

#delete unneeded files created by quickstart. we will replace it later by our project.
(tg2env)$ rm -rf ~/tg2env/molgears/molgears

Download molgears project from github:
https://github.com/admed/molgears

copy molgears directory to:
~/tg2env/molgears/


2. Build rdkit from source code with INCHI support:
https://github.com/rdkit/rdkit/blob/master/Docs/Book/Install.rst

copy rdkit directory to:
~/tg2env/lib/python2.X/site-packages/

3. Download razi from my fork:
https://github.com/admed/razi

copy razi/razi to: ~/tg2env/lib/python2.X/site-packages/

4. Install postgresql:
https://help.ubuntu.com/community/PostgreSQL

5. Build the catridge:
https://code.google.com/p/rdkit/wiki/BuildingTheCartridge

Create new databse and add catridge support to it:
https://rdkit.readthedocs.org/en/latest/Cartridge.html#reference-guide

6. Add information about your database to development.ini file:
Edit the file: ~/tg2env/molgears/development.ini and comment the line:
# sqlalchemy.url = sqlite:///%(here)s/devdata.db
Than uncomment the line:
sqlalchemy.url=postgres://username:password@hostname:port/databasename

and put your data like database user name, password, hosname, port and databasename to this line

7. Install additional libraries by pip:

first install pip:
(tg2env)$ sudo apt-get install pip

than additional libraries by using command:
(tg2env)$ pip install library_name

where libraries are:

- tw2.forms
- tw.forms
- Genshi
- zope.sqlalchemy
- webhelpers
- repoe.who
- repoze.who.plugins.sa
- psycopg2
- tgext.admin
- pillow
- paste
- xhtml2pdf
- xlwt
- xlrd
- numpy
- scipy
- matplotlib
- sqlalchemy_migrate

8. RUN your aplication:
(tg2env)$ python setup.py develop
(tg2env)$ gearbox setup-app
(tg2env)$ gearbox serve

than you can open your browser and go to address:
http://127.0.0.1:8080

login: manager
passwor: managepass


enjoy :)