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.
mkvirtualenv nanocompore -p python3.6
conda create -n nanocompore python=3.6
Nanocompore relies on a the following robustly maintained third party python libraries:
- numpy >= 1.16.0
- scipy >= 1.2.0
- tqdm >= 4.32.0
- pyfaidx >= 0.5.5
- matplotlib >= 3.1
- seaborn >= 0.9.0
- pandas >= 0.24.2
- statsmodels >= 0.9.0
- scikit-learn >= 0.21.2
- bedparse >= 0.2.2
The correct versions of packages are installed together with the software when using pip.
Option 1: Direct installation with pip from PyPi (recommended)
pip3 install nanocompore
Option 2: Direct installation with pip from github
To install the package with https/ssh you need pip>=19
pip3 install git+https://github.com/tleonardi/nanocompore.git
Option 3: 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/tleonardi/nanocompore.git # Enter in repo directory cd nanocompore # Install with pip3 pip3 install -e ./
Testing the installation (Optional)
nanocompore is installed in develop mode (Option 2) it is recommended to run the unit tests and integration tests to verify the installation. The test framework
pytest needs to be installed manually to run the test in the virtual environment where
NanoCompore is also installed.
pip install pytest
pytest in the directory where
nanocompore was downloaded.
If all the tests are successful you should get a similar output:
====================================== test session starts ======================================= platform linux -- Python 3.6.6, pytest-4.3.0, py-1.7.0, pluggy-0.8.1 rootdir: /home/aleg/Programming/nanocompore, inifile: collected 40 items tests/test_Integration.py ................. [ 42%] tests/test_SampCompDB.py .... [ 52%] tests/test_TxComp.py ............... [ 90%] tests/test_Whitelist.py .... [100%] ================================== 40 passed in 160.40 seconds ===================================