run_on_ukd.md

How to run on UKD computer

1. Install Python: https://www.python.org/downloads/

2. Go to the install location and find python.exe (e.g. C:\Users\YOURUSERNAME\AppData\Local\Programs\Python\Python312\python.exe)

3. Open command line, cd to your project, enter the path to the python.exe with -m venv YOURVENVNAME python=3.12 to create a virtual environment.

4. Run YOURVENVNAME\Scripts\activate

5. • Before you install any requirements with pip, run these: set HTTP_PROXY=http://ukd-proxy:80 and set HTTPS_PROXY=http://ukd-proxy:80

6. Install requirements with pip install -r requirements.txt --proxy=http://ukd-proxy:80

7. Every time you install anything with pip (or any other package), use the UKD Proxy!

8. Add proxy to git: git config --global http.proxy http://ukd.proxy:80

9. Clone Repository: git clone https://github.com/KatherLab/LLMAnonymizer.git

10. Install OCRmyPDF:

    • Refert to this guide: https://ocrmypdf.readthedocs.io/en/latest/installation.html#installing-on-windows

    • install chocolatey and install tesseract

    • Install Ghostscript on another computer in a custom location and copy this directory to the UKD computer. Set the PATH to include tesseract and ghostscript

    • Before you install OCRmyPDF with pip, run these: set HTTP_PROXY=http://ukd-proxy:80 and set HTTPS_PROXY=http://ukd-proxy:80

    • pip install ocrmypdf --proxy=http://ukd-proxy:80

    • set PATH to include both tesseract and ghostscript: set PATH=D:\Path\to\tesseract\;D:\Path\to\gs\bin;%PATH% You need to do this every time you logout / restart the computer! Only run this command once!

11. cd LLMAnonymizer

12. Open in VSCode / refer to the README on how to run.