Getting started (Windows)

Check your python version

First, open a Command Prompt.


To open Command Prompt, simply type ‘cmd’ in the search box of the Windows taskar.

easYPipe needs at least Python 3.6.

You may already have Python installed – you can check which version by doing:

C:\> python --version
C:\> py -V

If Python version is <3.6, install the latest Python 3 version. Download the latest python version Python downloads site. You can follow instructions here. But what you need is simply:

- Run the installer. You can do so by double-clicking python-<version>.exe in your Downloads folder.
- !!!! Check the box next to "Add Python <version> to PATH." It's at the bottom of the window.
- Install Now (customize installation not compulsory).
- Click Disable path length limit. This ensures that Python (and other apps) to use paths more than 260 characters in length.

Check that Python 3 has been correctly installed:

C:\> python --version
Python 3.9


C:\> py -V
Python 3.9

Software requirements

easYPipe is a pipeline that requires other software.


You need Phenix [1] installed and to modify PHENIX_PATH value in file accordingly.

Example for PHENIX_PATH in

PHENIX_PATH = r"C:\Users\myname\Phenix\phenix-installer-1.19.1-4122-intel-windows-x86_64"

Open Babel

Open Babel [2] is a chemical toolbox needed for ligands.

Install Open Babel GUI for Windows.

Example for BABEL_PATH in

BABEL_PATH = r"C:\Program Files\OpenBabel-3.1.1"



paths to these software have to be modified in file accordingly to your installation (see next step)


it might be wise to use LibreOffice [3] as many csv spreadsheets are generated by easYPipe and Excel does not handle the official csv format (i.e. comma-separated values) well for non-English speaking versions

Download and install easypipe package

Download the zip archive that should look like easypipe-1.4.2.tar.gz.

Go where is the archive and unzip:

C:\> tar -xvzf easypipe-1.4.2.tar.gz

Go to folder easypipe-1.4.2:

C:\> cd easypipe-1.4.2

Modify (open with a text editor like Notepad) file (in easypipe-1.4.2 folder), in particular ‘Software used by modules’ part since nothing will work without links to software.

Warning file modifications have to be done before installation !! If you want to modify it afterwards, just launch installation again. Use a basic text editor and not a word processing software !

Then install:

C:\> python install
C:\> py install

Check easypipe installation

You can test if installation is successfull doing:

$ -h

If you get no error but the help message, easypipe installation is successfull.

Depending on your python version, you may encountered some dependecies and conflict problems. Read carefully the error messages.

In case of the following error:

$ cffi>=1.4.2 distribution was not found and is required by PyNaCl

This command should help:

$ py -m pip install cffi

Uninstall easypipe package

To uninstall easypipe package properly, do:

C:\>  pip uninstall easypipe


‘py -m pip freeze’ lists the names of all python packages installed.