miRge-build is developed and tested on Linux environment.


  • miRge-build installation requires python 3.8 or newer
  • Bowtie v1.2.3 - please pick one based on your OS.
    • After downloading Bowtie, extract it (unzip,
    • Change directory to bowtie cd bowtie-1.2.3-linux-x86_64 and type pwd to get full path of the directory (pwd: present working directory).
    • Add that path to the environment PATH: export PATH=$PATH:"pwd <path> ".
      • Example: export PATH=$PATH:"/home/user/software/bowtie-1.2.3-linux-x86_64"
  • Requires scipy for enabling novel miRNA analysis python3.8 -m pip install --user scipy==1.4.1
  • Requires scikit-learn for enabling novel miRNA analysis python3.8 -m pip install scikit-learn==0.23.1
  • Requires biopython for parsing all input FASTA files python3.8 -m pip install biopython==1.77

Quick installation

The easiest way to install miRge-build is to use pip3 on the command line:

If you have root previlages, then install miRge-build as follows:

sudo python3.8 -m pip install miRge-build

if you have only user previlages:

python3.8 -m pip install --user miRge-build

This will download the software from PyPI (the Python packaging index), and install the miRge-build binary into $HOME/.local/bin. If an old version of miRge-build exists on your system, the --upgrade parameter is required in order to install a newer version. You can then run the program like this:

~/.local/bin/miRge-build --help

If you want to avoid typing the full path, add the directory $HOME/.local/bin to your $PATH environment variable.

Installation with conda

Yet to be implemented


To uninstall type:

pip uninstall miRge-build