A Java-based GUI application for submitting proteomics data to the PRIDE Archive and ProteomeXchange.
- Download: Use one of these options:
- Latest version: px-submission-tool-latest.zip
- Specific version: Visit GitHub Releases
- Universal link: Always points to the latest:
https://github.com/PRIDE-Archive/px-submission-tool/releases/latest/download/px-submission-tool-latest.zip
- Extract: Extract the zip file to a folder of your choice
- Launch: Follow the OS-specific launch instructions below
- Small Download: The tool is now only ~140MB (vs 400MB+ before)
- Auto-Download: Java 21 JRE is downloaded automatically if needed
- Smart Detection: Uses your system Java if it's version 21 or higher
- No Re-downloading: Once downloaded, JRE stays in the tool directory
- Internet Required: First run needs internet to download JRE (if system Java is too old)
- Extract the zip file completely
- Double-click
start.bat - First Run: If you don't have Java 21+, the tool will download it automatically (~250MB)
- Subsequent Runs: Uses the downloaded JRE (no re-downloading)
- Done! 🎉
- Quick Fix: Make sure JAR file is in the same folder as start.bat
- Manual Launch:
java -jar px-submission-tool-2.11.0.jar - No Internet: Install Java 21+ manually from Adoptium
- JRE Location: Downloaded JRE is stored in
jre-windows/folder
- Extract the zip file completely
- Run:
./start.sh - First Run: If you don't have Java 21+, the tool will download it automatically (~250MB)
- Subsequent Runs: Uses the downloaded JRE (no re-downloading)
- Done! 🎉
- Permission Fix:
chmod +x start.sh - Manual Launch:
java -jar px-submission-tool-2.11.0.jar - No Internet: Install Java 21+ manually from Adoptium
- JRE Location: Downloaded JRE is stored in
jre-macos/folder
- Extract the zip file completely
- Run:
./start.sh - First Run: If you don't have Java 21+, the tool will download it automatically (~250MB)
- Subsequent Runs: Uses the downloaded JRE (no re-downloading)
- Done! 🎉
- Permission Fix:
chmod +x start.sh - Manual Launch:
java -jar px-submission-tool-2.11.0.jar - No Internet: Install Java 21+ manually from Adoptium
- JRE Location: Downloaded JRE is stored in
jre-linux/folder
- Check System Java: If you have Java 21+, use it
- Download JRE: If system Java is too old, download Java 21 JRE (~250MB)
- Store Locally: JRE is saved in platform-specific folder:
- Windows:
jre-windows/ - macOS:
jre-macos/ - Linux:
jre-linux/
- Windows:
- Find Local JRE: Automatically detects downloaded JRE
- Skip Download: No re-downloading, instant startup
- Launch Application: Uses the local JRE
- ✅ Smaller initial download: ~140MB vs 400MB+
- ✅ Faster subsequent launches: No download time
- ✅ Offline capable: Works without internet after first run
- ✅ Cross-platform: Automatic platform detection
If you get permission errors, make the scripts executable:
chmod +x start.shThe tool automatically downloads Java 21 JRE if needed, but if you encounter issues:
- Download Java 21: Visit Adoptium
- Choose: OpenJDK 21 (JRE or JDK)
- Install: Follow platform-specific installation instructions
- Verify: Run
java -versionto confirm Java 21+ is installed - Launch: Run the tool again - it will use your system Java
If the tool previously downloaded a JRE but can't find it:
- Windows:
jre-windows\bin\java.exe -jar px-submission-tool-2.11.0.jar - macOS:
./jre-macos/Contents/Home/bin/java -jar px-submission-tool-2.11.0.jar - Linux:
./jre-linux/bin/java -jar px-submission-tool-2.11.0.jar
Set JAVA_HOME to point to your Java 21 installation:
- Windows:
set JAVA_HOME=C:\Program Files\Java\jdk-21 - macOS/Linux:
export JAVA_HOME=/path/to/java21
If Aspera or FTP transfers fail:
- The tool will suggest using Globus as an alternative
- Visit: https://www.ebi.ac.uk/pride/markdownpage/globus
- Globus provides reliable, high-speed file transfers
- If you get security warnings, run:
xattr -cr .in the tool directory - Or right-click
start.shand select "Open" to bypass Gatekeeper
px-submission-tool-2.11.0/
├── start.bat # Windows launcher
├── start.sh # Linux/macOS launcher
├── px-submission-tool-2.11.0.jar # Main application JAR
├── jre-windows/ # Windows JRE (downloaded on-demand)
├── jre-linux/ # Linux JRE (downloaded on-demand)
├── jre-macos/ # macOS JRE (downloaded on-demand)
├── aspera/ # Aspera transfer binaries
├── config/ # Configuration files
└── help/ # Help documentation
If you prefer to use your own Java 21 installation instead of the auto-downloaded JRE:
# Set JAVA_HOME to your Java 21 installation
export JAVA_HOME=/path/to/your/java21
java -jar px-submission-tool-2.11.0.jarThe tool automatically detects system proxy settings. To configure manually:
# Set proxy environment variables
export http_proxy=http://proxy.example.com:8080
export https_proxy=http://proxy.example.com:8080All application logs are consolidated into a single file:
- Location:
logs/px-submission.log - Contains: Transfer progress, API calls, errors, and debugging information
- Check Internet: Ensure you have internet connection for first-time JRE download
- Manual Install: Download Java 21 from Adoptium
- Firewall: Check if firewall is blocking the download
- Disk Space: Ensure you have at least 500MB free space for JRE download
chmod +x start.shxattr -cr .- Check for existing Java processes:
ps aux | grep java - Kill existing processes if needed
- Check for lock files in
~/.px-tool/directory
- Try the alternative transfer method suggested by the tool
- Use Globus as a reliable alternative: https://www.ebi.ac.uk/pride/markdownpage/globus
- Documentation: README
- Issues: GitHub Issues
- PRIDE Support: PRIDE Archive
- ProteomeXchange: ProteomeXchange
- Use: Send this file to support if you encounter issues
- Transfer failures: Use Globus alternative as suggested by the tool
- Login issues: Check your PRIDE credentials and network connectivity
- Progress bar stuck: Check the logs for detailed error information
- Check the logs in
logs/px-submission.log - Try the alternative transfer methods suggested by the tool
- Visit the PRIDE documentation
- Contact PRIDE support with your log file
- Built-in checker: The tool automatically checks for updates on startup
- GitHub integration: Uses GitHub Releases API for reliable update detection
- Smart notifications: Shows release notes and what's new in each version
- Universal links: Always provides the latest download link
- Versioned releases:
px-submission-tool-2.11.0.zip(specific version) - Latest release:
px-submission-tool-latest.zip(always current) - Universal link:
https://github.com/PRIDE-Archive/px-submission-tool/releases/latest/download/px-submission-tool-latest.zip
- Tool notification: You'll see an update dialog when a new version is available
- Review changes: Read what's new in the release notes
- Download: Click to open the GitHub release page
- Install: Download and extract the new version
- Restart: The tool may suggest restarting for major updates
- Always backup your submission data before updating
- Export any in-progress submissions
- Save your configuration files if customized
- Operating System: Windows 10+, macOS 10.14+, or Linux (64-bit)
- Memory: Minimum 4GB RAM, recommended 8GB+
- Disk Space: 2GB for installation + 500MB for JRE download (if needed), additional space for data files
- Network: Internet connection for data submission
- Java: Smart JRE management (auto-downloads Java 21 if needed)
For more information, visit the PRIDE Archive or ProteomeXchange