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Installation

This section will help you set up the necessary software and packages required to run SigProfilerSimulator.

Prerequisites

  • Python version >= 3.9
  • SigProfilerMatrixGenerator with a downloaded reference genome
  • Other dependencies are installed automatically during package installation

Installation

SigProfilerSimulator can be executed on any Windows/macOS/Unix system. First follow the SigProfilerMatrixGenerator guide for installing Python and pip. Next, follow the instructions below for the latest stable release or the current GitHub version.

Installation with pip

Install the latest SigProfilerSimulator PyPI version using pip: 

$ pip install SigProfilerSimulator

To upgrade an existing installation to the most recent version: 

$ pip install SigProfilerSimulator --upgrade

Install specific GitHub Release

First, download the zip file or clone the GitHub repository: 

$ git clone https://github.com/SigProfilerSuite/SigProfilerSimulator.git

Next, enter the downloaded directory and install the package: 

$ cd SigProfilerSimulator
$ pip install .

Download Reference Genome

SigProfilerSimulator requires a reference genome to perform simulations. To install the reference genome/s, use SigProfilerMatrixGenerator.

The last PyPI SigProfilerMatrixGenerator version is installed with SigProfilerSimulator by default. Install your desired reference genome from the command line/terminal as follows.

Installation from command line

$ SigProfilerMatrixGenerator install GRCh37

Installation from Python terminal

$ python
>>> from SigProfilerMatrixGenerator import install as genInstall
>>> genInstall.install('GRCh37', rsync=False, bash=True)

If you have a firewall on your server, you may need to install rsync and use the rsync=True parameter. If bash is not available, use bash=False.

For a full list of supported reference genomes, refer to the Supported Genomes section.