Sander W. van der Laan

@franfcunha could you potentially share your code on how you did this?

And if I manually compile, I get these messages. ``` user@macbook ~/git/PyHIST/src $ ls __init__.py graph_segmentation slide.py __pycache__ parser_input.py utility_functions.py (base) user@macbook ~/git/PyHIST/src $ cd graph_segmentation/ (base) user@macbook ~/git/PyHIST/src/graph_segmentation $...

The same happens with the example `svs`-image. ``` python3 ~/git/PyHIST/pyhist.py --content-threshold 0.05 --patch-size 64 --output-downsample 16 --info "verbose" --save-tilecrossed-image ~/git/PyHIST/use_case/GTEX-1117F-0126.svs 24-11-2021 13:39:13 [CRITICAL]: Compiling the graph segmentation algorithm... Compilation of...

Yes. That was it! Thanks. So practically: you need to run each within the folder where `PyHIST` is.

Could I change this behavior in the code? I would like to work in a different working directory, so keep `PyHIST` in a shared `software` folder. I am thinking I...

Did you update it to the master-branch?

Hi, @jinzhuangdou But... aren't these versions heavily dependent on the specific operating system too? I am also struggling to install and run the tool on my Mac (macOS Sonoma 14.4,...

Hi @jinzhuangdou , Because of the above, I tinkered with the original code. You did supply an example _input_ file, but you didn't provide the expected output-files. Do you have...

Hi @jinzhuangdou , The next step - imputation with `beagle` - yields a file which looks different from what is mentioned in the `readme.md` file. I don't know if that...

This is great @jinzhuangdou . This means the approach I took with respect to `samtools`, `vcftools`, and `bcftools` may be robust and thus `Monopogen.py` and `germline.py` could be adjusted to...