This site will allow users to search for gene transcription factors and find potential target genes.
The server and all of it's dependencies are installed on our AWS instance, so simply visit it's IP address in your browser. For login details and the IP address, check your email. Once you're logged in, cd into /srv/tftarget and you can begin development.
If you have the dependencies installed, simply run python manage.py runserver, then visit 127.0.0.1:8000 in a browser.
If you don't have the dependencies installed, start by getting Python 2.7.3. You can download it for free from python.org.
Now, you'll need to get pip, the Python Package Manager.
For all operating systems, these instructions will suffice.
On Debian-based Linux distributions, an easier way to get pip is to run apt-get install python-setuptools; easy_install pip.
Special note to Windows users: you may need to edit your path if the instruction above don't work, see this Stack Overflow discussion.
If you plan on doing any other Python projects, particularly Django ones, you should probably pip install virtualenv virtualenvwrapper and create a virtual environment for the project.
See the documentation for virtualenvwrapper if you think you'll do any other large Python projects, otherwise you can skip this step.
Now install the rest of the dependencies by running pip install -r requirements.txt.
The quickstart above is sufficient for getting a server that can run, but eventually you'll need to install MySQL and setup Django to use it.
MySQL can be downloaded from their website and installed by following the directions.
During install, you should be asked to create a password for the root user.
Do this, and don't forget the password, you will need it soon and may need it later in an emergency.
On Debian-based Linux distributions, an easier way to get MySQL is to run apt-get install mysql-server.
Once MySQL is installed, you'll need to get the Python library for talking to it.
If you're on a Debian-based Linux distribution, you can install it with apt-get install python-mysqldb.
Other Linux distributions should have a similar package available, but the Python MySQLdb library cannot be installed on Windows without having to edit a few files manually.
Talk to me (Joel Friedly) and I'll try to get you working on Windows.
If you're unsure whether or not your MySQLdb installation worked, open a Python interpreter and run import MySQLdb.
Once the Python library is installed, you'll need to create your tftarget MySQL user.
To do this, run mysql -uroot -p and enter the root password that you picked above, then input these SQL commands at the prompt, where $PASSWORD is a new password that you choose:
mysql> CREATE USER 'tftarget'@'localhost' IDENTIFIED BY '$PASSWORD'; mysql> CREATE DATABASE tftarget DEFAULT CHARACTER SET utf8 DEFAULT COLLATE utf8_general_ci; mysql> GRANT ALL PRIVILEGES ON tftarget.* to 'tftarget'@'localhost' WITH GRANT OPTION;
MySQL should tell you that each query was ok.
Exit the MySQL prompt and now create a file in this directory called local_settings.py.
Put the following lines into the file and save it, making up a secret key to use for hashing:
import settings settings.DATABASES['default']['PASSWORD'] = '$PASSWORD' settings.SECRET_KEY = "$SECRET_KEY"
Ensure that Django has access to the MySQL database by opening a Python interpreter with python manage.py shell and then running these commands:
>>> from search.models import TranscriptionFactor >>> tf = TranscriptionFactor(tf='E2F1') >>> tf.save() >>> tf.delete()
Databases complain whenever a table schema is changed, and anytime you make a change to a class in a models.py file it represents a change to a table schema.
South makes migrating table schemas easy, without losing your data.
Information on South can be found on their tutorial, and you should already have it installed if the pip install -r requirements.txt worked.
The first thing you'll need to do is run a python manage.py syncdb, and create a Django admin user by following the prompts.
Then, run this command for each app that we built, replacing $APP_NAME with the name of the app (currently we've only created one app, called search):
$ python manage.py migrate $APP_NAME
In order to load the latest SQL dump, run these commands, giving the root user's password at the prompt each time:
$ mysql -uroot -p tftarget < search_experiment_expt_type.sql $ mysql -uroot -p tftarget < search_experiment.sql $ mysql -uroot -p tftarget < search_experiment_transcription_factor.sql $ mysql -uroot -p tftarget < search_experimenttype.sql $ mysql -uroot -p tftarget < search_transcriptionfactor.sql
If you run into errors that rows are attempting to foreign key to other rows that don't exist when you're trying to import the data, read on.
Simply drop the table with DROP TABLE $TABLE_NAME and then try to import the data again using mysql -uroot -p tftarget < $TABLE_NAME.sql.
Depending on which table it was, you may need to drop some other tables first because of foreign key constraints.
The many-to-many lookup tables can always be dropped, and once those are gone, any of the others can be dropped.
The tables can be restored in any order (I think).
If this doesn't work, don't worry, we're just using fake data for now.
Do NOT do this on a production database.
The best introduction to Python that I know of is the Python Tutorial at python.org. Other highly recommended tutorials include Dive into Python and Learn Python the Hard Way.
The Django Tutorial is an excellent four-part starter series on Django. It will assume that you know at least a little Python though.