Purpose

If you are running cactus serially for a multi-way alignment, preparing SLURM submission scripts from the cactus-prepare output can be tedious. This script automates that process.

Requirements

• Python 3

Usage

Modify the information in align_header.txt to your liking. Then run:

python cactus_prepare_parser.py \
    --cactus-prepare slurm-cactus-prepare.stdout \
    --output-dir my-slurm-scripts

Then submit the resulting scripts. They are split into difference directories by task (pre-process, align, HAL merging).