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Source

STRique can be installed without root privileges as it's maintaining its dependencies by building required libraries from source in a user accessible path. Currently the following list of system wide packages is required to build STRique (names on macOS might be different):

  • git wget
  • gcc-6 g++-6 (C++14 support)
  • make cmake
  • python3-dev
  • zlib1g-dev, libbz2-dev

These packages are likely present in most production environments. Please also refer to the Dockerfile of the package repository for minimal system requirements.

Python3 macOS

While git, gcc and make are present on macOS, cmake and python3 might not be. If not already done consider installing the brew package management and run brew install cmake python3 afterwards. It can be necessary to modify your PATH variable to find the python3 interpreter. Before continuing with this guide make sure that either python --version or python3 --version yields the expected result of 3.x.x

Dependencies

Python 3.5 or higher

wheel cython
pomegranate
numpy, scipy, scikit-image
h5py

C++

SeqAn2
Pybind11

Dependencies get downloaded and build by the setup script.

Installation

Please consider to install STRique into a separate virtual environment to avoid conflicting dependencies with other packages or if you don't have root access. Update pip and install virtual environment:

python3 -m pip install --user --upgrade pip
python3 -m pip install --user virtualenv

Create a virtual python environment:

python3 -m venv /path/to/your/environment
cd /path/to/your/environment
source bin/activate

In order to download, build and install STRique, execute the following commands:

mkdir -p ~/src && cd ~/src
git clone --recursive https://github.com/giesselmann/STRique
cd STRique
pip3 install -r requirements.txt
python3 setup.py install

If the process didn't report any errors, continue in the test section to verify the installation.