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# Installation
## Create a clean virtual environment (optional but recommended)
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](https://virtualenvwrapper.readthedocs.io/en/latest/install.html):
```bash
mkvirtualenv pycoQC -p python3.6
workon pycoQC
```
With [conda](https://conda.io/projects/conda/en/latest/user-guide/install/index.html):
```bash
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
```bash
pip install pycoQC
```
You can also update to **unstable** development version from test.pypi repository
```bash
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**
```bash
# 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
```bash
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
```bash
# 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](contributing.md)).
```bash
# 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 ./
```
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