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 ./