TumGenomSim is a simulator that generates multi-regional tumor sequencing data. It has been tested on Ubuntu and RedHat linux, but should run without modifications on all other Unix-based platforms, including OS X.
Given the required dependencies, the installation should only require a few steps:
git clone https://github.com/hdetering/tumgenomsim.git mkdir tumgenomsim/build && cd tumgenomsim/build cmake .. make
The executable can be found at tumgenomsim/build/src/tgs.
Since most of the user parameters are provided in a config file, the command line arguments to run TumGenomSim are kept to a minimum. Where arguments overlap with the config file, the command line arguments override those in the file.
$ ./tgs -h
TumGenomSim 1.2.0
Available options:
-v [ --version ] print version string
-h [ --help ] print help message
-c [ --config ] arg config file
-t [ --tree ] arg file containing user defined clone tree (Newick
format)
-o [ --out-dir ] arg output directory
-p [ --threads ] arg (=1) number of parallel threads
-s [ --seed ] arg random seed
The command line parameters control the following aspects of a TumGenomSim run:
-v/--version: just print the program version and exit
-h/--help: print usage info
-c/--config: path to config file
-t/--tree: clone tree to use in simulation
-o/--output: path to output directory (will be created if not exists)
-p/--threads: how many threads to use in parallel execution
-s/--seed: seed to initialize random number generator
For a complete list of user parameters see the annotated example config.