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Installation

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

Prerequisites

  • Python version >= 3.9
  • SigProfilerMatrixGenerator with a downloaded reference genome (required to generate mutational matrices and simulations)
  • SigProfilerSimulator (required to generate the background model used for IMD threshold calculation)
  • Other dependencies are installed automatically during package installation

Installation

SigProfilerClusters 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 SigProfilerClusters PyPI version using pip: 

$ pip install SigProfilerClusters

To upgrade an existing installation to the most recent version: 

$ pip install SigProfilerClusters --upgrade

Install specific GitHub Release

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

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

Next, enter the downloaded directory and install the package: 

$ cd SigProfilerClusters
$ pip install .

Download Reference Genome

SigProfilerClusters requires a reference genome to generate simulations and mutational matrices. Current reference genomes supported include GRCh37, GRCh38, mm9, and mm10. To install the reference genome/s, you need to use SigProfilerMatrixGenerator.

The last PyPI SigProfilerMatrixGenerator version is installed with SigProfilerClusters by default. You can also install a specific version following the instructions in the SigProfilerMatrixGenerator Wiki.

Once SigProfilerMatrixGenerator is installed, 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. Similarly, if you do not have bash available, use bash=False.

In case you prefer to install a reference genome from a local copy: 

$ python
>>> from SigProfilerMatrixGenerator import install as genInstall
>>> genInstall.install('GRCh37', offline_files_path='path/to/directory/containing/GRCh37.tar.gz')