Installation

Installation¶

System Requirement¶

UMIche is advised to be installed within a conda environment, which makes it easier to work on multiple platforms, such as Windows (partial), Mac, and Linux. Owing to the exclusivity of Pysam to the Linux and Mac environments, UMIche does not work with BAM-related analysis in the Windows system.

PyPI (version 0.1.1 suggested!!)¶

umiche homepage on PyPI

# create a conda environment
conda create --name umiche python=3.11

# activate the conda environment
conda activate umiche

# the latest version
pip install umiche --upgrade

Conda¶

umiche homepage on Anaconda

# create a conda environment
conda create --name umiche python=3.11

# activate the conda environment
conda activate umiche

# the latest version
conda install jianfeng_sun::umiche

Docker¶

umiche homepage on Docker

docker pull 2003100127/umiche

Github¶

umiche homepage on Github

# create a conda environment
conda create --name umiche python=3.11

# activate the conda environment
conda activate umiche

# create a folder
mkdir project

# go to the folder
cd project

# fetch UMIche repository with the latest version
git clone https://github.com/2003100127/umiche.git

# enter this repository
cd umiche

# do the following command
pip install .
# or
python setup.py install