Brownotate

Brownotate is an application designed for generating a protein sequence database for a given species. It can be run as a command-line tool or as a web application using Flask.

Before setting up your own Brownotate server, you can try a demo version without installing anything. Simply contact me at browna@unistra.fr, and I will create an account for you on the server hosted at my institute.

Prerequisites

-Operating System: Linux (Ubuntu 22.04 or similar). Make sure to use a Linux server as Conda dependencies are not compatible with other operating systems.

Installation

Clone the Repository

First, clone the Brownotate repository:

git clone https://github.com/LSMBO/Brownotate.git
cd Brownotate

Install Conda

If you do not have Conda installed, follow these steps to install it:

1. Download Anaconda:

wget https://repo.anaconda.com/archive/Anaconda3-2024.06-1-Linux-x86_64.sh
chmod +x Anaconda3-2024.06-1-Linux-x86_64.sh
./Anaconda3-2024.06-1-Linux-x86_64.sh

Follow the instructions to complete the installation:

-Read and accept the terms by typing 'yes' -Choose the default installation location -Confirm updating your shell profile to initialize Conda automatically

2. Initialize Conda:

conda init

Create and Activate Conda Environments

Create and activate the required Conda environments:

For the br environment:

cd /path/to/Brownotate
conda env create -f environment_br.yml

For the sra-download environment:

cd /path/to/Brownotate
conda env create -f environment_sra_download.yml

Configure MongoDB

1. Download MongoDB Community Server:

Go to MongoDB Community Download, select:

• Version: 7.0.14 (current)
• Platform: Ubuntu 22.04 x64
• Package: Server

Or whichever matches your configuration.

Click on Download.

2. Install MongoDB:

sudo dpkg -i mongodb-org-server_7.0.14_amd64.deb

3. Start MongoDB:

sudo systemctl start mongod
sudo systemctl status mongod

4. Download MongoDB Shell:

Go to MongoDB Shell Download, select:

-Version: 2.3.0 -Platform: Debian (10+) / Ubuntu (18.04+) x64 -Package: deb

Or whichever matches your configuration.

Click on Download.

5. Install MongoDB Shell:

sudo dpkg -i mongodb-mongosh_2.3.0_amd64.deb

6. Configure MongoDB:

mongosh
use brownotate-db
db.createCollection("users")
db.createCollection("dbsearch")
db.createCollection("runs")
db.createCollection("processes")

Configure config.json

Edit the config.json file located in the root directory of the project:

{
  "email": "",
  "MONGO_URI": "",
  "BROWNOTATE_PATH": "",
  "BROWNOTATE_ENV_PATH": "",
  "SRA_DOWNLOAD_ENV_PATH": ""
}

• MONGO_URI: This follows the format mongodb://<ip>:<port>/brownotate-db. You can find the correct URI by running the mongosh command in your terminal. The IP is typically localhost and the port is usually 27017.
• BROWNOTATE_PATH: This should be the directory where you cloned the Brownotate repository.
• BROWNOTATE_ENV_PATH: Use the command conda info --envs to locate the path to the br Conda environment.
• SRA_DOWNLOAD_ENV_PATH: Use the command conda info --envs to locate the path to the sra-download Conda environment.

Running Brownotate

1. Web Application:

To set up the Brownotate web application, you need to configure both the client from (https://github.com/LSMBO/brownotate-app) and the backend (https://github.com/LSMBO/Brownotate). Brownotate The web client for Brownotate is hosted in a separate repository. Follow the instructions in the Brownotate web client repository (https://github.com/LSMBO/brownotate-app) to install and configure the client. The client is responsible for interacting with the user and sending requests to the Brownotate backend.

Once the client is set up, you need to launch the Brownotate backend, which is a Flask-based server that handles requests from the client and executes commands. This backend is served using Gunicorn, a Python WSGI HTTP server optimized for handling concurrent connections. It has already been installed in the br Conda environment.

Use the following command to start the Flask server:

conda activate br
gunicorn -w 4 --worker-class eventlet --bind 0.0.0.0:8800 --timeout 2592000 run_flask:app 

The IP 0.0.0.0 allows the server to accept requests from any IP address. The port 8800 corresponds to the port on which the server listens for requests from the client.

Other scripts

• database_admin.py

Adds a user to the mongodb database. Works with -email and -password. If the email is already in the database, this changes the password.

Example:

python /path/to/Brownotate/database_admin.py -email test@email.com -password 48141514

Note: The password is encrypted using bcrypt before being stored in the database for added security.

• clear_working_dir.py

Proposes to delete old run working directories. Data can quickly accumulate, so a bit of tidying up from time to time is not a bad idea. Using input() methods, the script proposes to delete each run one after the other.

Example:

python /path/to/Brownotate/clear_working_dir.py