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Installation

Create a clean virtual environment

Ideally, before installation, create a clean python3.6 virtual environment to deploy the package. Python 2 is not supported. For example one can use conda or virtualenvwrapper.

With virtualenvwrapper:

mkvirtualenv pyBioTools -p python3.6

workon pyBioTools

With conda:

conda create -n pyBioTools python=3.6

conda activate pyBioTools

Dependencies

Nanocompore only relies robustly maintained third party python libraries listed in the setup.py file The correct versions of packages are installed together with the software when using pip or conda

Option 1: Installation with pip from pypi

Install or upgrade the package with pip from pypi

# First installation
pip install pyBioTools

# Update to last version
pip install pyBioTools --upgrade

Option 2: Installation with conda from anaconda

Install or upgrade the package with pip from pypi

# First installation
conda install -c aleg -c anaconda -c conda-forge -c bioconda pybiotools

# Update to last version
conda update pybiotools

Option 3: Installation with pip from Github

Or from github to get the last version

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

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

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

Option 4: 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/pyBioTools.git

# Enter in repo directory
cd pyBioTools

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

# Install with pip3
pip3 install -e ./