slurmbot 0.2.2

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 🤖

SlurmBot is a minimalistic tool to wrap and execute sbatch commands from Python scripts with optional Conda environment management, useful for integrating Slurm job submissions directly into your workflows. Based on jbatch.

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).

• ⚙️ 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

Install SlurmBot via pip: 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)