G-CAT Runner

G-CAT Runner is a task runner for G-CAT Workflow and others.

Setup

1. Install

pip install gcat_runner

How to use

1. Bash script

For example, run.sh

set -x

echo "success"

2. Config file

With YAML format, for example, conf.yml

log_dir: .           # log output directory
qsub_option: ''      # qsub/slurm command options (invalid with bash-runner)
retry_count: 1       # number for retry 
runner: bash         # choose in ['qsub', 'drmaa', 'slurm', 'bash', 'openpbs']
                     # qsub: task runs with 'qsub -sync'
                     # drmaa: task runs with drmaa library
                     # slurm: task runs with 'sbatch --wait'
                     # bash: task runs with 'bash'
                     # openpbs: task runs with 'qsub -Wblock=true'

3. Run

gcat_runner run.sh conf.yml

options:
--interval seconds: Randomly modify job submission within the specified range of 0 to the specified number of seconds.