README.md

cactusBenchmarks

cactusBenchmarks is an infrastructure for reproducibly running different versions and configurations of progressiveCactus on a variety of test sets.

Installation

First, download the test regions (which are too large to store in git):

./testRegions/download_test_regions.sh

Running with Docker

Use bin/run.sh:

./bin/run.sh [OPTIONS] testLabel

You can run any number of tests simultaneously, with different versions and config files, without the runs interfering with one another.

Running without Docker

Ensure you're in the progressiveCactus environment, and that mafComparator and the dotplot scripts are in your PATH. Use bin/runBenchmarks.py:

./bin/runBenchmarks.py [OPTIONS] progressiveCactusDir testRegionsDir testLabel

You should only run one instance of runBenchmarks.py at a time per progressive cactus directory.

Options

--tests TESTS

list of tests to run (comma-separated)

--progressiveCactusBranch PROGRESSIVECACTUSBRANCH

branch of progressiveCactus to switch to

--cactusBranch CACTUSBRANCH

branch of cactus to switch to

--cactusConfigFile CACTUSCONFIGFILE

config xml to use instead of default. When using Docker, this is copied into the container, so it may be safely modified after the container starts running.

--outputDir OUTPUTDIR

dir to place test results in

--stats

output stats file with jobTree stats