-

README.md

@@ -4,45 +4,58 @@
 [![Documentation Status](https://readthedocs.org/projects/rhapsody/badge/?version=latest)](https://rhapsody.readthedocs.io/en/latest/?badge=latest)
 
 # Rhapsody
-Python program, based on ProDy, for pathogenicity prediction of human missense variants.
+Python program, based on ProDy, for pathogenicity prediction of human
+missense variants.
 
 ## Install latest published version using pip
-Rhapsody is published on [PyPI](https://pypi.org/). To install Rhapsody, please use pip in the terminal:
+Rhapsody is published on [PyPI](https://pypi.org/). To install Rhapsody,
+please use pip in the terminal:
 ```console
-$ pip install -U prody-rhapsody
+pip install -U prody-rhapsody
 ```
-It might be necessary to manually install the DSSP program, for instance by typing on Linux:
+It might be necessary to manually install the DSSP program, for instance
+by typing on Linux:
 ```console
-$ sudo apt install dssp
+sudo apt install dssp
 ```
 
 ## Install from source
 Rhapsody is written in pure Python so no local compilation is needed.
 
-To install all needed dependencies, we strongly suggest to use Conda and create a new environment with:
+To install all needed dependencies, we strongly suggest to use Conda and create
+a new environment with:
 ```console
-conda create -n rhapsody python=3 numpy scikit-learn requests pyparsing matplotlib
+conda create -n rhapsody python=3 numpy scikit-learn requests pyparsing
+matplotlib biopython
+
 conda activate rhapsody
-pip install biopython prody
+
+pip install prody
+
 conda install -c salilab dssp
 ```
 
-After cloning/forking the Rhapsody repository, you can permanently add the repository path to the conda environment with:
+After cloning/forking the Rhapsody repository, you can permanently add the
+repository path to the conda environment with:
 ```console
 conda develop path/to/local/repository
 ```
 
-If not using Conda, you can manually install all dependencies and then add the repository location to the `PYTHONPATH` environmental variable. For example, on Linux simply add the following line to your `~/.bashrc`:
+If not using Conda, you can manually install all dependencies and then add
+the repository location to the `PYTHONPATH` environmental variable. For
+example, on Linux simply add the following line to your `~/.bashrc`:
 ```console
 export PYTHONPATH="path/to/local/repository/:$PYTHONPATH"
 ```
 
-If you are running on Windows, please follow this [tutorial](https://stackoverflow.com/a/4855685).
+If you are running on Windows, please follow this
+[tutorial](https://stackoverflow.com/a/4855685).
 
 ## Running initial setup
 
 After installation, please run:
 ```console
 import rhapsody as rd
+
 rd.initialSetup()
 ```