I am facing a problem with the installation and opening of the px-submission tool. Can anyone give me a complete step-by-step process to run in Windows 10? Java is a recent version.
I tried with manual manual-based step, but was unable to do so.
Adnan Majeed
Download the Tool: Go to the official PRIDE-Archive GitHub page or the PRIDE Submission Tool page on the EBI website (e.g., https://github.com/PRIDE-Archive/px-submission-tool or https://www.ebi.ac.uk/pride/markdownpage/pridesubmissiontool). Look for the "DOWNLOAD TOOL" or "Quick Download" link. The tool is typically released as a zipped file. Verify Java Installation (and install if needed): Open your command line/terminal: On Windows: Search for "cmd" or "Command Prompt" in the Start menu. On macOS/Linux: Open the "Terminal" application. Check Java version: Type java -version and press Enter. Expected Output: You should see something like java version "21.x.x" (where x are sub-versions). If Java is not found or is an older version: You'll see an error message like "java -version is not recognized..." or a version lower than 21. You'll need to install Java JRE 21 or higher. You can download it from the official Oracle website or adoptopenjdk.net (for OpenJDK). Follow the installation instructions for your operating system. Important: After installing Java, it's often recommended to restart your machine to ensure environment variables are correctly set. Unzip the Downloaded File: Locate the downloaded zipped file (e.g., px-submission-tool-.zip). Unzip its contents to a directory on your computer. Make sure the directory path does not contain any blank spaces or special characters. Inside the unzipped folder, you'll find a .jar file (e.g., px-submission-tool-.jar) and a lib folder. The lib folder contains all necessary libraries. Run the PX-Submission Tool: Method 1: Double-clicking (Recommended for most users) Navigate to the unzipped folder. Double-click on the px-submission-tool-.jar file. This should launch the application wizard. Method 2: Command Line (Useful for troubleshooting or if double-clicking doesn't work) Open your command line/terminal. Navigate to the directory where you unzipped the tool using the cd command: cd (Replace with the actual path to your unzipped folder). Run the tool using the Java command: java -jar px-submission-tool-.jar(Replace with the actual version number of your downloaded tool).
System Requirements:
- Java: The PX-Submission tool is a Java-based application. You need Java JRE 21 or above to run it. Most computers should have Java installed, but it's crucial to have the correct version.
- Operating System: It has been tested on Windows 10, Windows 7, Windows Vista, Linux, and Mac OS X, and should work on other platforms as well.
Installation Steps:
Troubleshooting Tips:
- "Java is not recognized..." error: This confirms Java is not installed or its environment variables are not set correctly. Reinstall Java and ensure you follow any post-installation steps (like setting JAVA_HOME if required, though for basic running, usually just installing Java is enough).
- Tool doesn't open/crashes: Check the px_submission.log file located in the px-submission-tool/log folder (within your unzipped directory) for error messages. This log file can provide valuable clues. Ensure your Java version is 21 or higher. Make sure the path to the tool directory doesn't have spaces or unusual characters.
- macOS specific: You might need to adjust your privacy and security settings to allow the application to run, especially if you get a warning about it being from an "unidentified developer."
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