BGE library curation tool

This BGE library curation tool is a standalone programm to be used by taxonomic experts to curate records from BOLD database pre-curated by this bioinformatic pipeline to be part of a european reference library for animal species in europe. The results will be used to create a European reference library as part of the EU project Biodiversity Genomics Europe.

Installation

This repository contains the Linux- and Mac-Version. For Windows, please go to BGE_library_curation_tool_win

Please also download the corresponding database files for the families you wish to curate from this website!

You will also find there a video tutorial and FAQs.

Dependencies

• node.js
• npm

🔧 Installation Guide (Linux & macOS)

Follow these steps to set up the tool on your system:

---

1. Copy or Clone the Repository

git clone https://github.com/your-username/your-repo-name.git

and navigate to the folder: BGE_library_curation_tool

cd BGE_library_curation_tool

Start the tool, if npm is already installed. Otherwise, please continue with point 2.

npm start

open any browser (firefox, Chrome etc) go to localhost:3000

2. Remove Old Dependencies (if any)

rm -rf node_modules package-lock.json
npm cache clean --force

3. Check Your System Architecture

uname -m                # Should return: arm64
node -p "process.arch"  # Should return: arm64

If you see x64, you're using Rosetta. Install the native ARM version of Node with nvm:

nvm install node
nvm use node

4. Install Dependencies

npm install

If you run into issues with sqlite3, install it from source:

npm install sqlite3 --build-from-source

5. Start the Tool

npm start

Then open your browser at:

http://localhost:3000

✅ Notes

This works for both Linux and macOS.

Requires Node.js (v18 or newer) and npm.

Use nvm to manage Node versions easily.    

Usage

To use the tool, a dataset is required that originates from the library curation pipeline.
The data is provided to users in the form of a database file (data.db). Extract the folder you have downloaded and place the .db file within the sub-folder data/.

BGE_library_curation_tool/
├── data/       # Please place the .db files within this subfolder
├── logs/       # Once you have finished your curation, please copy the changes.log file and sent it back to (curation_tool@snsb.de and kuehbandner@snsb.de)
├── public/
├── package.json
├── server.js
└── user_manual_windows.html # user manaual for windows, but beside installation and starting everything should work the same way.

Refresh http://localhost:3000 in your browser and you should be able to select the taxa you wish to curate from the drowdown menue. Please continue with the user_manual_windows.html.