Download and install¶
This section covers the necessary steps to install and run SNPknock. Below is a list of required dependencies, along with additional software recommendations. The following instructions are for Linux and Mac users. It may be possible to compile the sources under Windows, but we are not providing support for Windows.
SNPknock is currently under development and it should be considered to be of beta quality. Any feedback will be greatly appreciated.
Dependencies¶
Python 2.7.5 or later
- NumPy 1.13.1 or later
- A high-level, optimized scientific computing Python library.
- Cython 0.26 or later
- Cython is a language that is a fusion of Python and C. It allows us to write fast code using Python and C syntax, so that it easier to read and maintain. You need Cython if you are building the development source code (and that is what you have to do at the moment, because we don’t yet have a release).
- gcc 5.3.0 or later
- The GNU Compiler Collection (GCC) is a compiler system produced by the GNU Project supporting various programming languages. Here, it is needed to compile the core of the SNPknock source code that is written in C++.
Building from source code¶
The source code is available on GitHub.
Clone the repository and enter the source directory. Then, you can build the SNPknock package with:
python setup.py build
To install, simply do:
sudo python setup.py install
Note
As with any python installation, this will install the modules in your system python site-packages directory (which is why you need sudo). Many of us prefer to install development packages in a local directory so as to leave the system python alone. This is mearly a preference, nothing will go wrong if you install using the sudo method. To install for the current user, use:
python setup.py install --user
Installing via pip¶
SNPknock can be easily installed through pip:
sudo pip install SNPknock
Note
As with any python installation, this will install the modules in your system python site-packages directory (which is why you need sudo). Many of us prefer to install development packages in a local directory so as to leave the system python alone. This is mearly a preference, nothing will go wrong if you install using the sudo method. To install for the current user, use:
pip install SNPknock --user