https://github.com/vmikk/phylotwin_react
PhyloTwin-GUI
https://github.com/vmikk/phylotwin_react
Last synced: 3 months ago
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PhyloTwin-GUI
- Host: GitHub
- URL: https://github.com/vmikk/phylotwin_react
- Owner: vmikk
- License: mit
- Created: 2025-01-03T09:28:36.000Z (5 months ago)
- Default Branch: main
- Last Pushed: 2025-02-17T11:29:51.000Z (3 months ago)
- Last Synced: 2025-02-17T12:29:29.673Z (3 months ago)
- Language: JavaScript
- Homepage:
- Size: 3.18 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
## PhyloTwin-GUI - GUI for GBIF occurrence data processing pipeline
#### Other components of the workflow:
- https://github.com/vmikk/phylotwin-preprocessor
- https://github.com/vmikk/phylotwin
### Local development
Install Java using SDKMAN (required for Nextflow):
```bash
# Install SDKMAN
curl -s https://get.sdkman.io | bash
# .. Open a new terminal
# and install Java
sdk install java 17.0.10-tem
java -version
```
Install Nextflow and pull the core pipeline:
```bash
# Install Nextflow
curl -s https://get.nextflow.io | bash
# Pull the core pipeline
nextflow pull vmikk/phylotwin -r main
```
Pull pipeline dependencies:
```bash
docker pull vmikk/phylotwin:0.6.0
docker pull vmikk/biodiverse:1.6.0
```
Install Node.js and npm:
```bash
# Download and install nvm
curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.40.1/install.sh | bash
# Download and install Node.js
nvm install 22
## Verify the Node.js version
node -v # v22.12.0
nvm current # v22.12.0
## Verify npm version
npm -v # 10.9.0
```
Install project dependencies:
```bash
## Install project dependencies for the client
cd client
npm install --legacy-peer-deps
## Install project dependencies for the server
cd ../server
npm install --legacy-peer-deps
```
## Start the development servers - need two terminal tabs
```bash
# Terminal 1 (for the backend) - In the server directory
npm run dev
# nodemon server.js # assuming server.js is your entry point
# Terminal 2 (for the frontend) - In the client directory
npm start
```
Frontend is at http://localhost:3000
Backend API is at http://localhost:5000
## Debugging
To set development mode and enable detailed logs:
```bash
export NODE_ENV=development
```
Production mode logs only errors and warnings:
```bash
export NODE_ENV=production
```
To see the logs in the browser:
- Open developer tools
- Go to the Console tab
- You'll see all client-side logs when submitting the form
In the server terminal, one may find detailed logs about:
- Job initialization
- File contents
- Nextflow command being executed
- Process output and errors
## Previous version of the GUI
The first version of the GUI was developed by Thomas Stjernegaard Jeppesen at GBIF
#### React web app - frontend
https://github.com/gbif/phylonext-ui
#### Backend
https://github.com/gbif/phylonext-ws