Update instructions for venv setup

Co-authored-by: Sebastian Urchs <surchs@users.noreply.github.com>

README.md

@@ -109,13 +109,15 @@ The following scripts are used:
 - `parallel_bagel.sh`
 
 ### Steps
-1. Activate a new Python environment and install the dependencies for this repo with `pip install -r requirements.txt`.
+1. (Optional) create a new Python environment with `python -m venv my_env`.
+2. Activate your python environment with `source ./my_env/bin/activate`
+3. Install the dependencies with `pip install -r requirements.txt`
 
-2. Get the latest version of the `bagel-cli` from Docker Hub: `docker pull neurobagel/bagelcli:latest`
+4. Get the latest version of the `bagel-cli` from Docker Hub: `docker pull neurobagel/bagelcli:latest`
 
-3. Create a directory called `inputs` in the repository root that contains all the datasets that will be processed with the CLI.
+5. Create a directory called `inputs` in the repository root that contains all the datasets that will be processed with the CLI.
 
-4. To run the CLI in parallel across the datasets in `inputs/`, double check that the directory paths used by `parallel_bagel.sh` and `run_bagel_cli.sh` are correct, then run:
+5. To run the CLI in parallel across the datasets in `inputs/`, double check that the directory paths used by `parallel_bagel.sh` and `run_bagel_cli.sh` are correct, then run:
 ```bash
 ./parallel_bagel.sh
 ```