Required softwares and dependencies

Before you install GRAFIMO the user must have installed:

• VG, v1.27.1 or later (https://github.com/vgteam/vg)
• Tabix (https://github.com/samtools/htslib)
• Graphviz (https://graphviz.org/)

The user should ensure that they are all reachable in Unix PATH.

Note that is suggested to use samtools tabix and not the one coming with VG. If the user is not sure about which tabix is running, he/she can type which tabix, to retrieve which is the currently used tabix.

GRAFIMO is written in both Python3 and Cython. Thus, the user will need Cython to be installed to correctly build GRAFIMO. Cython can be obtained via pip

pip3 install Cython

To build GRAFIMO are used setuptools and wheel. The user should make sure he/she has the latest version of both setuptools and wheel

python3 -m pip install --user --upgrade setuptools wheel

GRAFIMO depends on some Python packages. If the user's machine does not satisfy the dependencies, building GRAFIMO from source and via pip they should be automatically solved.

To install all the required packages:

pip3 install pandas
pip3 install numpy
pip3 install statsmodels
pip3 install sphinx
pip3 install numba