BLAST Web App Deployment with Flask and MySQL

Overview

This article documents a practical Bioinformatics BLAST Web App deployment workflow for an SFTS Flask application on Linux. The system uses Flask as the web backend, MySQL as the database, BLAST for sequence search, uWSGI as the Python application server, and Nginx as the reverse proxy.

User browser -> Nginx port 80 -> uWSGI -> Flask -> MySQL / BLAST

Environment

Server: Cloud server
OS: Linux
Web framework: Flask
Database: MySQL
ORM: SQLAlchemy
Application server: uWSGI
Reverse proxy: Nginx
Bioinformatics tool: NCBI BLAST+
HTTP port: 80
Flask internal port: 5000

Step 1: Open the Web Port

The web application needs to be reachable through HTTP.

Protocol: TCP
Port: 80
Source: 0.0.0.0/0

The request path is:

public internet -> cloud firewall -> Linux server -> Nginx -> Flask

Step 2: Deployment Architecture

Nginx listens on port 80
Nginx proxies requests to Flask on 127.0.0.1:5000
uWSGI runs the Flask application
Flask queries MySQL and calls BLAST when needed

Step 3: Prepare the Python Project Environment

Example project path:

/www/server/python_project/vhost/sfts

Activate the environment:

source /www/server/panel/sfts/bin/activate
source /www/server/python_project/vhost/sfts.env

Install dependencies:

pip install -r requirements.txt

Step 4: Fix uWSGI Command Not Found

One recorded error was:

failed to run command 'uwsgi': No such file or directory

Install uWSGI inside the active environment:

pip install uwsgi

If installation fails with:

fatal error: Python.h: No such file or directory

install Python development headers and GCC:

yum install python3-devel gcc -y

Step 5: Configure Nginx Reverse Proxy

location / {
    proxy_pass http://127.0.0.1:5000;
}

Reload Nginx:

nginx -t
systemctl reload nginx

Step 6: Install NCBI BLAST+

cd /usr/local
tar -xzf ncbi-blast-2.17.0+-x64-linux.tar.gz

Add BLAST to PATH:

echo 'export PATH=/usr/local/ncbi-blast-2.17.0+/bin:$PATH' >> ~/.bashrc
source ~/.bashrc

Verify:

blastn -version

NCBI BLAST+ can be downloaded from the official NCBI BLAST+ executables directory.

Step 7: Build the BLAST Database

cd /www/wwwroot/sfts/fasta
makeblastdb -in sfts-sequence.fasta -dbtype nucl -out sfts-sequence-db

Expected output files include:

.nin
.nsq
.nhr

Step 8: Configure BLAST Paths in Flask

BLASTN_EXE = "/usr/local/ncbi-blast-2.17.0+/bin/blastn"
BLAST_DB = "/www/wwwroot/sfts/fasta/sfts-sequence-db"

Using absolute paths avoids environment differences between the shell, uWSGI, and system services.

Step 9: Fix MySQL Permission Problems

One recorded MySQL error was:

SELECT command denied to user 'sfts-db'@'localhost'

Temporary broad grant:

GRANT ALL PRIVILEGES ON *.* TO 'sfts-db'@'localhost' WITH GRANT OPTION;
FLUSH PRIVILEGES;

Safer production-style grant:

GRANT SELECT, INSERT, UPDATE, DELETE ON sfts.* TO 'sfts-db'@'localhost';
FLUSH PRIVILEGES;

Step 10: Check Runtime Logs

/www/wwwlogs/python/sfts/uwsgi.log

When the application fails, check uWSGI startup logs, Python import errors, MySQL connection errors, BLAST command errors, and Nginx logs.

Common Problems

Website Cannot Open

cloud firewall port 80
Linux firewall
Nginx status
Nginx reverse proxy
uWSGI process
Flask app startup

uWSGI Cannot Start

Check whether uwsgi exists in the virtual environment and whether the service uses the correct Python environment.

Python.h Missing During uWSGI Installation

yum install python3-devel gcc -y

BLAST Command Works in Shell but Not in Flask

Use absolute paths for both BLAST executable and database files.

BLAST Is Slow

limit API frequency
add request throttling
cache repeated search results
use threading lock if concurrent BLAST jobs conflict
optimize FASTA database size

Final Conclusion

This SFTS deployment combines Flask, MySQL, BLAST, uWSGI, and Nginx on Linux.

open port 80 in the cloud firewall
use Nginx as the public entry point
run Flask behind uWSGI
install uWSGI inside the correct virtual environment
use absolute paths for BLAST
fix MySQL permissions carefully
check uWSGI and Nginx logs when debugging

After these pieces are configured correctly, the browser can access the Flask application through Nginx, and the backend can perform database queries and BLAST sequence searches reliably.

FAQ

What is a BLAST web app?

A BLAST web app is a browser-based bioinformatics tool that lets users submit biological sequences, run BLAST searches on the server, and view matched sequence results through a web interface.

Can Flask be used for a bioinformatics sequence search system?

Yes. Flask can provide the web interface and API layer, while NCBI BLAST+ performs sequence search and MySQL stores application data or sequence metadata.

Why use absolute paths for BLAST in Flask?

Absolute paths avoid environment differences between interactive shell sessions, uWSGI processes, system services, and Nginx-managed deployments.

Why does BLAST work in the shell but fail in Flask?

This usually happens because the Flask or uWSGI process does not inherit the same PATH, environment variables, permissions, or working directory as the interactive shell.

How should a Flask BLAST app be deployed on Linux?

A common production setup is Nginx as the public reverse proxy, uWSGI as the Python application server, Flask as the web backend, MySQL as the database, and NCBI BLAST+ installed with absolute executable and database paths.

Need Help Deploying a Bioinformatics Web App?

This note is based on a real Flask, MySQL, BLAST, uWSGI, and Nginx deployment workflow. If you need help building or deploying a BLAST web app, sequence search portal, research database system, Flask API, Linux web service, or scientific data processing tool, GetModNest can provide practical development, troubleshooting, and deployment support.

Email: info@getmodnest.com