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choosehappy / HoverFast

Blazing fast nuclei segmentation for brightfield Whole Slide Images
BSD 3-Clause "New" or "Revised" License
29 stars 4 forks source link

How to invoke HoverFast on command line #3

Closed roberts10 closed 2 months ago

roberts10 commented 2 months ago

How do I invoke HoverFast from the command line? The documentation says to use the command, "HoverFast" followed by options. Like:

HoverFast --version

However, HoverFast isn't a command on my $PATH.

For context, I didn't have Docker available. So installed like:

git clone https://github.com/choosehappy/HoverFast.git cd HoverFast pip install .

Thanks so much! It's looks like a really amazing tool.

petroslk commented 2 months ago

Hey there!

Happy to see you're using HoverFast. Could you provide me with some information on the Operating System you are using and how you installed the tool? Was is done through conda or did you install it directly on the machine?

With this info I should be able to guide you a bit better and tell you exactly how to run it successfully!

Cheers,

Petros

roberts10 commented 2 months ago

Installing in my /home directory of an HPC, which is Linux Red Hat 8. It doesn't have conda (or miniconda). And I don't have Docker permissions.

I created a python virtual environment with python 3.11. Then I ran:

git clone https://github.com/choosehappy/HoverFast.git cd HoverFast pip install .

If Docker or Conda is required, I'm sure I could get my sys admin to install with those.

Thanks!

petroslk commented 2 months ago

Thanks for the details! It sounds like the HoverFast command might not be recognized because the entry point script wasn’t added to your $PATH when you installed it.

Here’s how you can try to resolve this:

  1. Ensure the installation was successful:
    After running pip install ., you should see that the installation completed without errors. You can verify this by listing the installed packages in your virtual environment with pip list and checking for HoverFast.

  2. Check the Scripts Directory: The HoverFast command is likely installed in the Scripts or bin directory of your virtual environment. You can find it by navigating to the bin directory in your virtual environment:

    cd /path/to/your/virtualenv/bin
ls

  3. Add the Script to Your PATH: If the HoverFast command is present in the bin directory but not recognized globally, you can add the directory to your $PATH temporarily:

    export PATH=/path/to/your/virtualenv/bin:$PATH

    After this, you should be able to run HoverFast directly from the command line.

Now, you should be able to invoke HoverFast using the command you mentioned, like HoverFast --version.

Keep in mind, for HPC environments, singularity (apptainer) might be more suitable since it does not require the same level of priviliges, so that might also be worth a try!

Let me know if this helps or if you run into any other issues!

Cheers,
Petros

roberts10 commented 2 months ago

That worked great

Just had to add the virtual env's /bin to my $PATH, like you said.

Thanks again