pybeast 0.3.0

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pyBEAST

PyBEAST helps with running BEAST with best practices. Configure a beast run in a reproducible manner can be time consuming. pyBEAST is designed to making running beast as simple as possible.

Install

Install pybeast with pip (requires python -V >= 3.7).

pip install pybeast

Command line interface

Basic usage

pybeast beast.xml

1. Create output folder and run command
2. Ensures the run is self-contained and reproducible.

pybeast --run bash beast.xml

The --run flag tells pybeast how to run the run.sh file.

SLURM example

This example using the SLURM template in the examples folder to submit the beast run as a job.

pybeast --run sbatch --template examples/slurm.template examples/beast.xml

At a minimum the template must contain {{BEAST}} key. This will be replaced with the beast2 run command.

Here we use the -v (--template-variable) option to request 4 cpus.

pybeast --run sbatch --template examples/slurm.template -v cpus-per-task=4 exmaples/beast.xml

Default template variables can be specified in the template in the format {{<key>=<value>}} e.g. {{cpus-per-task=4}}.

dynamic variables

PyBEAST uses dynamic-beast to create dynamic xml files that can be modified at runtime.

Here we use the -d (--dynamic-variable) option to set the chain length to 1000000.

pybeast -d mcmc.chainLength=1000000 examples/beast.xml

The dynamic variables are saved to a .json file in the run directory. This file can be further edited before runtime. At run time the values in the JSON file will be used in the analysis.

Example

BETS

Use pybeast + feast to run BETS.

ALIGNMENT=${1?Must provide an ALIGNMENT}
for XML_FILE in $(ls examples/BETS-templates/*)
do  
    GROUP_NAME="BETS/$(basename "${ALIGNMENT}" .fasta)/$(basename "${XML_FILE}" .xml)"
    pybeast \
        --run sbatch \
        --overwrite \
        --threads 8 \
        --duplicates 3 \
        --template examples/slurm.template \
        -v cpus-per-task=8 \
        --group $GROUP_NAME \
        -d "alignment=$ALIGNMENT" \
        -d "Date.delimiter=_" \
        -d "Date.dateFormat=yyyy/M/dd" \
        --ps \
        -d "ps.nrOfSteps=50" \
        -d "ps.chainLength=250000" \
        -d "ps.rootdir={{run_directory}}/logs" \
        $XML_FILE
done