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.

Note

Please note that starting from version 0.1.5, pysam is no longer a required dependency when installing umiche. This means you can install umiche on any operating system. If you need to use pysam, you should install umiche on a non-Windows system and then install pysam separately. Please refer to the documentation for instructions on how to install it.

PyPI (highly recommended, see the latest version)

umiche homepage on PyPI

Note

Please make sure to use the latest version of umiche, as earlier versions may contain bugs. If you do not include the --upgrade flag during installation, you might encounter issues.

# 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