Install Miniconda: https://docs.conda.io/en/latest/miniconda.html
Then, type in the following commands in your terminal:
$ conda create --name <whatever-name-you-want>
$ conda activate <whatever-name-you-want>
Resource for Conda: https://docs.conda.io/projects/conda/en/4.6.0/_downloads/52a95608c49671267e40c689e0bc00ca/conda-cheatsheet.pdf
In your terminal with the environment activated, type in the command:
$ pip install pipreqs
- Try pip3 if pip doesn't work
In your terminal with the environment activated, type in the command:
$ pip install -r requirements.txt
- pdftotext
- Install instructions here: https://pypi.org/project/pdftotext/
Copy the contents of config.template.ini into a new file called config.ini and modify to fit your needs
- For VSCode, make sure your Python interpreter is set to the path of your environment before running. You can check the by opening the Command Palette (Ctrl or Cmd + Shift + P) and clicking 'Python: Select Interpreter'. Click the refresh button if you don't see the environment path you created.
I'm getting "[SSL: CERTIFICATE_VERIFY_FAILED]"! Take a look at page 49, here: https://ncbi-taxonomist.readthedocs.io/_/downloads/en/stable/pdf/