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Installation

Ideally, before installation, create a clean python3.6+ virtual environment to deploy the package. Earlier version of Python3 should also work but Python 2 is not supported. For example one can use conda or virtualenvwrapper.

With virtualenvwrapper:

mkvirtualenv pycoQC -p python3.6
workon pycoQC

With conda:

conda create -n pycoQC python=3.6
conda activate pycoQC

Dependencies

pycoQC relies on a few robustly maintained third party libraries listed below. The correct versions of the packages are installed together with the software when using pip.

  • numpy>=1.13
  • scipy>=1.1
  • pandas>=0.23
  • plotly>=3.4
  • jinja2>=2.10
  • h5py>=2.8.0
  • tqdm>=4.23'

Option 1: Installation with pip from pypi

Install or upgrade the package with pip from pypi

pip install pycoQC

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

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

Option 2: Installation with conda from Anacounda 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 -c anaconda -c bioconda -c conda-forge pycoqc=[VERSION]

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

conda install -c aleg_dev -c anaconda -c bioconda -c conda-forge pycoqc=[VERSION]

Option 3: Installation with pip from Github

To get the last stable (master) or bleeding edge (dev) version

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

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

# Update to last version
pip install git+https://github.com/a-slide/pycoQC.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 stable repo locally
git clone https://github.com/a-slide/pycoQC.git

# bleeding edge branch
git clone --branch dev https://github.com/a-slide/pycoQC.git

# Enter in repo directory
cd pycoQC

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

# Install with pip3
pip3 install -e ./