Utilities for MI-TO analyses. This package is still under active development. To use functions and modules perform the following steps:
- Install mamba package manager (https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html)
- Choose one of the following environment recipes:
envs
├── environment.yml # minimal, OSX
├── environment_latest_OSX.yml # Latest, OSX
├── environment_mito_utils.yml # Verified, Linux
└── environment_preprocessing.yml # Minimal, only for preprocessing- Reproduce the environment with:
mamba env create -f <chosen environment name>.yml -n <your conda env name>- cassiopeia and MQuad packages need manual installation. After reproducing the environment:
mamba activate <chosen environment name>
pip install mquad
pip install git+https://github.com/YosefLab/Cassiopeia@master#egg=cassiopeia-lineage- After these steps, activate the new environment and cd to the main mito_utils repo path. Make the repo path visible to python import system.
cd <path to mito_utils clone>
mamba develop .
- Fire a python terminal and verify successfull installation of all packages.
from mito_utils import *