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Installation - Python

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

Prerequisites

  • Internet Connection
  • Python - v3.4+
  • pandas - any version (automatically downloaded when you install SigProfilerMatrixGenerator)
  • Wget - v1.9
  • SigProfilerPlotting - latest version (automatically downloaded when you install SigProfilerMatrixGenerator)
  • Reference genomes - latest version (must be downloaded separately after installation)

Upgrades

If there is an updated version of the tool that has been released, use the following command within Terminal or the Command Line:

pip install SigProfilerMatrixGenerator --upgrade

This will upgrade the tool to its latest version.

Mac/Unix Installation

For Mac/OSX systems, the use of a package manager like Conda is recommended to simplify environment setup.

Check Python Version

Check that you have the required python version by opening Terminal (Cmd + Space, type terminal, and hit return) and entering:

python --version

By default, OSX systems come with a version of Python installed at /usr/bin/python. This system version of Python is currently Python 2.

If you have multiple versions of Python installed, try:

python3 --version

You should see output like: 

Python 3.7.3

Follow Python Installation instructions to download the most recent version if you do not have v3.4 or higher.

Installation instructions for Conda through the Anaconda distribution can be found at Anaconda Installation.

Check pip

Check if you have pip installed:

pip --version

You should see output similar to: 

pip 19.0.1 from /Library/Frameworks/SomeFilePath/

This tells you which version of pip is currently installed, and which version of Python it is set up to install packages for.

Install SigProfilerMatrixGenerator

Now that you've successfully downloaded all the required software, install SigProfilerMatrixGenerator using pip:

pip install SigProfilerMatrixGenerator

Windows Installation

Check Python Version

By default, Windows systems do not come with Python installed. Check if you have Python by opening Command Prompt (Win + R, type cmd, and press Enter) and entering:

python --version

If you have multiple versions of Python installed, try:

python3 --version

If you know you have Python 3.4+ installed but get an error like: 

'python' is not recognized as an internal or external command

Then Python has not been added to the PATH environmental variable. Add it with:

setx PATH "%PATH%;[path_to_python where .exe file is]"

Follow Python Installation to download Python for your operating system. Make sure to check the "Add Python to PATH" box during installation.

Check pip

Check if you have pip installed:

pip --version

If pip is not recognized, add it to PATH:

setx PATH "%PATH%;[path_to_python]\Scripts\"

Install SigProfilerMatrixGenerator

pip install SigProfilerMatrixGenerator

Reference Genome Installation

Prior to use of SigProfilerMatrixGenerator, reference genome files need to be installed.

Install your desired reference genome from the command line as follows:

python3
>>> from SigProfilerMatrixGenerator import install as genInstall
>>> genInstall.install('GRCh37', bash=True)

This example installs the human GRCh37 assembly reference files. You can install any of the available genome assemblies.

If the server has a firewall that blocks wget, use the rsync parameter:

>>> genInstall.install('GRCh37', rsync=False)

Note: The installation process saves custom reference files for all chromosomes in the genome assembly, requiring ~3 GB of storage per genome. This step could take some time due to the large file sizes.