scripts/README.md

In Nik-Zainal-Group/signature.tools.lib: signature.tools.lib

signature.tools.lib scripts

Introduction

This folder includes scripts to perform analysis using the R package signature.tools.lib in unix command line style, without having to write R code.

Currently available scripts are:

• signatureFit: mutational signatures analysis using Fit or FitMS. This is a wrapper for the signatureFit_pipeline R function.
• hrDetect: HRDetect pipeline script. This is a wrapper for the HRDetect_pipeline R function.
• genomeChart: visualisation of somatic variants using a circle diagram and other graphs like mutational catalogues.
• solutionSelectionForFitMS: change selection criteria for FitMS alternative rare signature solutions and/or select solutions manually.

You can use the flag -h to access a list of options for each script, for example hrDetect -h.

Install in your PATH

You can move these scripts to a directory in your PATH, so that it can be used from the command line like any other program.

For example, you can create a bin directory in your home directory:

mkdir ~/bin

And add it to your path:

export PATH=~/bin:$PATH

You can add the above line to your ~/.bashrc file so you don't have to type it every time. Then, you can simply copy the files:

cd /path/to/where/you/downloaded/signature.tools.lib/scripts/
cp signatureFit ~/bin/
cp hrDetect ~/bin/
cp genomeChart ~/bin/
cp solutionSelectionForFitMS ~/bin/

Alternatively, you can create a symbolic link:

cd ~/bin/
ln -s /path/to/where/you/downloaded/signature.tools.lib/scripts/signatureFit
ln -s /path/to/where/you/downloaded/signature.tools.lib/scripts/hrDetect
ln -s /path/to/where/you/downloaded/signature.tools.lib/scripts/genomeChart
ln -s /path/to/where/you/downloaded/signature.tools.lib/scripts/solutionSelectionForFitMS

You should now have the scripts working anywhere in your command line.

Nik-Zainal-Group/signature.tools.lib documentation built on April 13, 2025, 5:50 p.m.