PX Submission Tool

A Java-based GUI application for submitting proteomics data to the PRIDE Archive and ProteomeXchange.

🚀 Quick Start

Download & Extract

1. 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
2. Extract: Extract the zip file to a folder of your choice
3. Launch: Follow the OS-specific launch instructions below

📦 Smart JRE Management

• 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)

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🖥️ Windows Users

1. Extract the zip file completely
2. Double-click start.bat
3. First Run: If you don't have Java 21+, the tool will download it automatically (~250MB)
4. Subsequent Runs: Uses the downloaded JRE (no re-downloading)
5. Done! 🎉

Windows Issues?

• Quick Fix: Make sure JAR file is in the same folder as start.bat
• Manual Launch: java -jar px-submission-tool-2.11.1.jar
• No Internet: Install Java 21+ manually from Adoptium
• JRE Location: Downloaded JRE is stored in jre-windows/ folder

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🍎 macOS Users

1. Extract the zip file completely
2. Run: ./start.sh
3. First Run: If you don't have Java 21+, the tool will download it automatically (~250MB)
4. Subsequent Runs: Uses the downloaded JRE (no re-downloading)
5. Done! 🎉

macOS Issues?

• Permission Fix: chmod +x start.sh
• Manual Launch: java -jar px-submission-tool-2.11.1.jar
• No Internet: Install Java 21+ manually from Adoptium
• JRE Location: Downloaded JRE is stored in jre-macos/ folder

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🐧 Linux Users

1. Extract the zip file completely
2. Run: ./start.sh
3. First Run: If you don't have Java 21+, the tool will download it automatically (~250MB)
4. Subsequent Runs: Uses the downloaded JRE (no re-downloading)
5. Done! 🎉

Linux Issues?

• Permission Fix: chmod +x start.sh
• Manual Launch: java -jar px-submission-tool-2.11.1.jar
• No Internet: Install Java 21+ manually from Adoptium
• JRE Location: Downloaded JRE is stored in jre-linux/ folder

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🔧 How Smart JRE Management Works

First Run (with internet):

1. Check System Java: If you have Java 21+, use it
2. Download JRE: If system Java is too old, download Java 21 JRE (~250MB)
3. Store Locally: JRE is saved in platform-specific folder:
   • Windows: jre-windows/
   • macOS: jre-macos/
   • Linux: jre-linux/

Subsequent Runs:

1. Find Local JRE: Automatically detects downloaded JRE
2. Skip Download: No re-downloading, instant startup
3. Launch Application: Uses the local JRE

Benefits:

• ✅ 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

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⚠️ Troubleshooting

Permission Denied Errors (Linux/macOS)

If you get permission errors, make the scripts executable:

chmod +x start.sh

Java Not Found or Download Failed

The tool automatically downloads Java 21 JRE if needed, but if you encounter issues:

Option 1: Manual Java Installation (Recommended)

1. Download Java 21: Visit Adoptium
2. Choose: OpenJDK 21 (JRE or JDK)
3. Install: Follow platform-specific installation instructions
4. Verify: Run java -version to confirm Java 21+ is installed
5. Launch: Run the tool again - it will use your system Java

Option 2: Use Downloaded JRE

If the tool previously downloaded a JRE but can't find it:

• Windows: jre-windows\bin\java.exe -jar px-submission-tool-2.11.1.jar
• macOS: ./jre-macos/Contents/Home/bin/java -jar px-submission-tool-2.11.1.jar
• Linux: ./jre-linux/bin/java -jar px-submission-tool-2.11.1.jar

Option 3: Environment Variables

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

Transfer Method Failures

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

macOS Security Warnings

• If you get security warnings, run: xattr -cr . in the tool directory
• Or right-click start.sh and select "Open" to bypass Gatekeeper

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📁 File Structure

px-submission-tool-2.11.1/
├── start.bat                        # Windows launcher
├── start.sh                         # Linux/macOS launcher
├── px-submission-tool-2.11.1.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

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🔧 Advanced Usage

Custom Java Installation

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-2.11.1.jar

Proxy Configuration

The 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:8080

Logging

All application logs are consolidated into a single file:

• Location: logs/px-submission.log
• Contains: Transfer progress, API calls, errors, and debugging information

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🆘 Troubleshooting

Common Issues

"Java not found" or "JRE download failed"

1. Check Internet: Ensure you have internet connection for first-time JRE download
2. Manual Install: Download Java 21 from Adoptium
3. Firewall: Check if firewall is blocking the download
4. Disk Space: Ensure you have at least 500MB free space for JRE download

"Permission denied" (macOS/Linux)

chmod +x start.sh

"Security warning" (macOS)

xattr -cr .

"Another instance is running"

1. Check for existing Java processes: ps aux | grep java
2. Kill existing processes if needed
3. Check for lock files in ~/.px-tool/ directory

Transfer failures (Aspera/FTP)

• Try the alternative transfer method suggested by the tool
• Use Globus as a reliable alternative: https://www.ebi.ac.uk/pride/markdownpage/globus

Getting Help

• Documentation: README
• Issues: GitHub Issues
• PRIDE Support: PRIDE Archive
• ProteomeXchange: ProteomeXchange
• Use: Send this file to support if you encounter issues

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📞 Support

Common 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

Getting Help

1. Check the logs in logs/px-submission.log
2. Try the alternative transfer methods suggested by the tool
3. Visit the PRIDE documentation
4. Contact PRIDE support with your log file

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🔄 Updates

Automatic Update Checking

• 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

Download Options

• Versioned releases: px-submission-tool-2.11.1.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

Update Process

1. Tool notification: You'll see an update dialog when a new version is available
2. Review changes: Read what's new in the release notes
3. Download: Click to open the GitHub release page
4. Install: Download and extract the new version
5. Restart: The tool may suggest restarting for major updates

Backup Recommendations

• Always backup your submission data before updating
• Export any in-progress submissions
• Save your configuration files if customized

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📋 System Requirements

• 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)

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For more information, visit the PRIDE Archive or ProteomeXchange