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Installation

Ideally, before installation, create a clean python3.6+ virtual environment to deploy the package. Earlier version of Python 3 should also work (not tested) but Python 2 is not supported. For example one can use conda or virtualenvwrapper.

With virtualenvwrapper:

mkvirtualenv NanoCount -p python3.6
workon NanoCount

With conda:

conda create -n NanoCount python=3.6
conda activate NanoCount

Dependencies

Minimap2 is not a direct dependency but is required to generate the BAM alignment required by NanoCount. Alternatively, other aligners might be used but NanoCount requires the optional AS flag to be set.

NanoCount only relies on a few robustly maintained third party python libraries which are installed together with the software when using pip or conda.

Install or upgrade the package with pip from pypi

pip install NanoCount

You can also update to the unstable development version from test.pypi repository

pip install --index-url https://test.pypi.org/simple/ NanoCount -U

Option 2: Installation with conda from Anaconda cloud

If you want to be sure to get the last version don't forget to add my channel and to specify the last version number

# First installation
conda install -c aleg nanocount=[VERSION]

You can also get the unstable development version from my dev channel

conda update -c aleg_dev nanocount=[VERSION]

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/NanoCount.git

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

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

# Enter in repo directory
cd NanoCount

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

# Install with pip3
pip3 install -e ./