Command Line

This page explains how to run Teaser from the command-line. This may be preferable to the web interface for some users, e.g. when working with a cluster or testing multiple data sets at once.

Benchmark Configuration File

Benchmarks are defined as a YAML configuration file. In this file you define data sets, mappers and parameter settings, and can adapt the evaluation itself. Teaser expects configuration files to be placed in the setups directory. To see how the various aspects of Teaser are controlled in a benchmark configuration file, see the following pages:

• Configuring Data Sets
• Configuring and using Mappers
• Configuring and using Parameter Sets

Running Teaser from the Command Line

To run Teaser from the command line, you need to supply the benchmark configuration file as argument:

./teaser.py example_ecoli.yaml

Where example_ecoli.yaml is the name of your benchmark configuration file.

The default directory for benchmark results is reports. Simulated read data and intermediate files will be placed in the tests_generated directory.

Command-Line Parameters

While most aspects of Teaser are controlled through the configuration file, there is a number of useful command-line options:

Parameter	Description
--mappers	Comma-separated list of read mappers to test (overwrites test_mappers field in configuration)
--parameters	Comma-separated list of parameter sets to test (overwrites test_parameters field in configuration)
--listmappers	List available read mappers and exit
--listparameters	List available parameter sets and exit
--forcegen	Override existing data sets. Use this to update data sets after changing simulation parameters.
--forcerun	Force re-evaluating all mappers, even if cached results exist
--measurecputime	Measure CPU time of mappers (default: wall-clock time)
--threads	Mapper thread count (default: set in configuration)
--exportreads	Export per-read analysis results as CSV
--nocleanup	Keep mapper output (SAM) files after evaluating
--reportname	Overwrites the name of the subdirectory in reports/ where results will be placed

For a full list of available command-line options, run Teaser with ./teaser.py --help.