Tark (Transcript Archive)

Tark (Transcript Archive)

An archive of all transcripts and its sequences from Ensembl, RefSeq and other sources. Provides RESTful data access through endpoints and also provides tools to visualize the data and compare the transcripts.

Requirements

• Python 3.6
• MySQL 5.6+

Installation

Clone the project from git

git clone https://github.com/Ensembl/tark.git

Create the Python environment (using virtualenv or python3 -m venv or any environment tool)

python3 -m venv virtualenv
source ./virtualenv/bin/activate

cd tark
pip install -r requirements.txt 

Provide the right credentials to connect to the tark database in secrets.py (created from secrets_template.py)

cp tark/tark/settings/secrets_template.py tark/tark/settings/secrets.py

Run the migrate step with --fake-initial (No need to run the migrations as the database is already there and it is not managed by Django)

cd tark/
./manage.py migrate --fake-initial

Start the development server cd tark/tark

 ./manage.py runserver localhost:9000

Check in the browsesr

http://localhost:9000/

Run all the tests in the package:

./manage.py test --settings=tark.settings.test

Using Docker

To run the app using docker, build and then run the image

docker build -t tark_app .

docker run -p 8000:8000 tark_app