This section presents and distributes code I have written and used for already published projects, or for projects that are about to be published in a near future.
Beagle_optimiser is a program written in Python that takes an XML input file prepared for BEAST, and finds the beagle option that will result in the shortest analysis time of that file. You can find out more about the program in the open laboratory notebook, and download the code from github. The program has the following functions:
mats@Slartibartfasts:~/project/beagle/test$ ./beagle_optimiser_0.9 -h Usage: beagle_optimiser_0.9.2 [-r] [-q] [-d] [--nogpu] [-f] FILE [-t] NAME [-n] N -i [file1 file2 ..] Options: --version show program's version number and exit -h, --help show this help message and exit -q, --quiet Minimum or no output to STDOUT -r, --run Run beast with the best speed settings immediately after the test -f FILE, --file=FILE Write output to FILE [bo_output.txt] -t NAME, --tmpdir=NAME Name of temporary directory for output files. This directory will be removed after the beagle tests are done if the --dev flag was not invoked [.bss_tmp] -n N, --ngen=N Chainlength for the Beast runs  --nogpu Do not use the "-Beagle_GPU" flag in the test -d, --dev Produce more output to STDOUT and save all temporary files -i, --input Followed by one or several input files
Output from the program looks like this:
_______________________________________ File: benchmark1.xml Sequences: 1441 Sites: 987 Unique patterns: 593 _______________________________________ Beast option: Time: -beagle_SSE 199.66 seconds -beagle_CPU 204.72 seconds -beagle_instances 2 211.04 seconds -beagle_instances 10 223.12 seconds -beagle_instances 8 227.52 seconds -beagle_instances 4 233.74 seconds -beagle_instances 12 237.6 seconds -beagle_instances 16 245.73 seconds -beagle_instances 14 253.28 seconds -beagle_GPU 263.08 seconds Native library 386.7 seconds -java 389.06 seconds _______________________________________
- Use a random seed when the "-r" option is used.
- Make BO work with MrBayes 3.2
- Test different beagle options in combination (is that relevant?)