Viral Instrant Mutation Viewer

About

Instant Variant is a web-service bioinformatics software. The goal of this project is to propose a bioinformatics tool for structural protein studies. Under CeCCIL license.

Usage

The project is deployed with apache2 service (via this link https://vimver.afmb.univ-mrs.fr/).

1. Paste your SARS-CoV2 related genomic sequence in the input box. Then press the 'Blast it' button underneath.

2. Press the newly appeared button to jump to the result.

3. Press the 'pick' button to acces the alignements for the corresponding line in the table.

Requirements

We have implemented this project in python 3.8+, along with three python packages :

• Python Django framework
• Biopython
• logomaker
• numpy

Installation

(Recomended for developpers or django user's)

1. The code is available via the following github repository: https://github.com/wildevince/ViralOceanView.git.

git clone https://github.com/wildevince/ViralOceanView.git

Verify your python version

python3 --version

install the required packages

python3 -m pip install -r requirements.txt

Verify your django version

python3 -m  django --version

2. We recommande to install the project with a python virtual environment.

3. If needed to verify your python version and install the required packages.

4. 'Settings.py' file is missing two information : the SECRET_KEY and INSTALLED_APPS.

Configuration

Create a new django project, and verify those lines :

• Declare apps in settings.py:

INSTALLED_APPS = [
    'OceanViewer.apps.OceanviewerConfig',
    'OceanFinder.apps.OceanfinderConfig',
    ...

• 'whitenoise' necessary for static files:

MIDDLEWARE = [
    ...
    'whitenoise.middleware.WhiteNoiseMiddleware',
]

• specify some paths often used in the code:

BASE_DIR = path.dirname(path.dirname(path.abspath(__file__)))
Temp_DIR = path.dirname(path.abspath(__file__))

STATIC_URL = '/static/'
STATICFILES_DIRS = (path.join(BASE_DIR, 'ViralOceanView', 'static'),)


DATATEST = path.join(path.dirname(BASE_DIR), "data_test") 

MEDIA_URL = 'file/'
MEDIA_ROOT = path.join(BASE_DIR, 'ViralOceanView', 'file')

DATABASE = path.join(MEDIA_ROOT, "dataBase_local")  

Deployment

We used a apache2 server for the deployment.

Citation

work in progress

Contacts

vincent.wilde@univ-amu.fr