Web 4D-QSAR

Open source web system to generate and validate QSAR modules.

Requirements

The Web 4D-QSAR was built and tested using Ubuntu 16.04 LTS but it should run without problems in any Linux distribution that supports the following softwares:

• Git >= ?
• Python >= 3
• Pip
• Virtualenvwrapper >= ?
• PostgreSQL >= 9.3
• RabbitMQ >= 3.3.1
• Gromacs >= 4.6.5
• LQTAGridPy
• dos2unix

Preparing the machine (Ubuntu 16.04 LTS)

* It should be automated using Puppet

Development requirements

• build-essential/cmake
• git
• python/python-dev/python-pip
• rabbitmq-server

$ sudo apt-get install build-essential cmake git python python-dev python-pip rabbitmq-server dos2unix

• virtualenvwrapper

$ pip install virtualenvwrapper

$ echo "export WORKON_HOME=$HOME/.virtualenvs" >> ~/.bashrc
$ echo "source /usr/local/bin/virtualenvwrapper.sh" >> ~/.bashrc

or

$ export WORKON_HOME=$HOME/.virtualenvs
$ export PROJECT_HOME=$HOME/devel
$ export /usr/local/bin/virtualenvwrapper.sh

Dynamic requirements

Gromacs

$ sudo apt-get install gromacs

Topolbuild

$ cd /tmp
$ wget -nv http://www.gromacs.org/@api/deki/files/93/=topolbuild1_3.tgz -O topolbuild1_3.tgz
$ tar xvfz topolbuild1_3.tgz
$ cd topolbuild1_3/src
$ make
$ sudo cp -r /tmp/topolbuild1_3 /opt
$ sudo chmod a+x /opt/topolbuild1_3/src/topolbuild
$ sudo ln -s /opt/topolbuild1_3/src/topolbuild /usr/bin/topolbuild

Installing and running Web 4D-QSAR

Clonning the repository

Clone the Web 4D-QSAR git repository and enter the project folder:

$ git clone https://github.com/rougeth/web-4d-qsar && cd web-4d-qsar

Preparing the environment

• Use virtualenvwrapper to create a virtual environment for python:

  $ mkvirtualenv web-4d-qsar -p path_to_python3

  In Ubuntu 16.04, the path to python 3 is /usr/bin/python3

• To access the virtualenv you just created: $ workon qsar Note that you will see the name of the environment in the PS1 variable: (env_name) $

• Install the required Python packages (you need to have the env activated and be at requirements folder):

  $ pip install -r requirements.txt

---

For the next steps, you must be at src/ folder.

Preparing the database

$ python manage.py makemigrations

No need of creating superuser.

Running Django

$ python manage.py runserver

Preparing Celery

Open a new terminal, access the virtualenv that was created with $ workon web-4d-qsar and go to src/ folder.

Running RabbitMQ

$ sudo rabbitmq-server -detached

Running worker

$ celery -A web-4d-qsar worker -l info

Now, go to your favorite browser, type http://127.0.0.1:8000 and see the celery working.