

Installation

Create a clean virtual environment

Ideally, before installation, create a clean python3.5+ virtual environment to deploy the package. Python 2 is not supported. For example one can use conda or virtualenvwrapper.

With virtualenvwrapper:

mkvirtualenv NanopolishComp -p python3.6

With conda:

conda create -n NanopolishComp python=3.6

Ideally, you might also want to install Nanopolish in the same virtual environment so you can pipe nanopolish output directly into NanopolishComp

Dependencies

Nanopolish 0.10+ is not a direct dependency but is required to generate the files used by several commands from this package

Nanocompore relies on a the following robustly maintained third party python libraries:

• numpy>=1.14.0
• tqdm>=4.23.4

The correct versions of packages are installed together with the software when using pip.

Option 1: Installation with pip from pypi

Install or upgrade the package with pip from pypi

# First installation
pip install NanopolishComp

# Update to last version
pip install NanopolishComp --upgrade

Option 2: Installation with pip from Github

Or from github to get the last version

# First installation
pip install git+https://github.com/a-slide/NanopolishComp.git

# First installation bleeding edge
pip install git+https://github.com/a-slide/NanopolishComp.git@dev

# Update to last version
pip install git+https://github.com/a-slide/NanopolishComp.git --upgrade

Option 3: Clone the repository and install locally in develop mode

With this option, the package will be locally installed in editable or develop mode. This allows the package to be both installed and editable in project form. This is the recommended option if you wish to modify the code and/or participate to the development of the package (see contribution guidelines).

# Clone repo localy
git clone https://github.com/a-slide/NanopolishComp.git

# Enter in repo directory
cd NanopolishComp

# Make setup.py executable
chmod u+x setup.py

# Install with pip3
pip3 install -e ./