slurmbot 0.2.3

Simple tool to wrap and execute sbatch commands from `python` scripts or `Jupyter Notebook` cells with `conda` envs and config files. Secure and reproducible

SlurmBot 🤖

Simple tool to wrap and execute sbatch commands from python scripts or Jupyter Notebook cells with conda envs and config files. Less mess, more reproducibility and security (if published to GitHub, for instance). Based on jbatch.

• ⚙️ Config Files: Create config files in YAML format and reuse them. Make a default.yaml in ~/.config/slurmbot/default.yaml
• 🐍 Python Variables: Easily integrate Python variables into your Slurm job commands.
• 🛠️ Conda: Activate Conda environments with the conda property.

Installation

pip install slurmbot

Example

from slurmbot import SlurmBot 
sb = SlurmBot() # using default yaml from ~/.config/slurmbot/default.yaml, if exists OR specify path to config
samples = ["SRR000001", "SRR000002"]
for sample in samples:
	sb.run(f"fasterq-dump {sample}", conda="ngs", mem=4, cpus=4, dry=True, v=2)