Slurmify

Slurmify is a lightweight, high-performance CLI tool written in Go that automates the creation of Slurm batch scripts (.sbatch) from a simple list of commands. It is designed for high-throughput computing, automatically handling job naming, log directory management, and command formatting.

Features

• Batch Generation: Converts a text file of commands into individual .sbatch files efficiently.
• Smart Naming: Automatically derives meaningful job names from input files or output flags.
• Safe Defaults: Creates organized output (./Sbatch) and log (./Logs) directories with secure permissions.
• Pretty Printing: Formats complex, multi-line commands with proper line continuation (\) for readability.
• Shell Safety: Correctly handles quoting for arguments containing spaces and preserves shell operators (>, |, >>).

Installation

Pre-compiled Binary

Download the latest release from the Releases Page.

Build from Source

Go 1.25+ required.

Clone the repo and use Make to build the versioned binary:

git clone https://github.com/Vanishborn/slurmify.git
cd slurmify
make

Usage

Prepare a text file (e.g., commands.txt) containing one command per line:

bwa mem -t 16 ref.fa sample1.fq > sample1.sam
samtools sort -o sample1.sorted.bam sample1.sam
fastqc --outdir ./QC sample2.fastq.gz

Run slurmify:

./slurmify -I commands.txt -A my_account

Generated Output

The tool will create a ./Sbatch directory containing scripts like sample1.sbatch.

Example Content (sample1.sbatch):

#!/bin/bash
#SBATCH --job-name=sample1
#SBATCH --account=my_account
#SBATCH --partition=standard
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=4G
#SBATCH --time=01:00:00
#SBATCH --output=./Logs/sample1_%j.out
#SBATCH --error=./Logs/sample1_%j.err

set -euo pipefail
echo "[$(date)] Job $SLURM_JOB_ID running on $(hostname)"

# Command
bwa mem \
  -t 16 \
  ref.fa \
  sample1.fq \
  > sample1.sam

Configuration Flags

Flag	Description	Default	Required
-I	Input text file with commands	-	Yes
-A	Slurm account name	-	Yes
-O	Output directory for .sbatch files	./Sbatch	No
-L	Directory for Slurm logs (.out/.err)	./Logs	No
-P	Slurm partition	standard	No
-C	CPUs per task	1	No
-M	Memory per task	4G	No
-T	Walltime (Format: HH:MM:SS)	01:00:00	No
-G	GRES string	-	No
-E	Email for notifications	-	No
-J	Job name prefix	job	No
-m	Environment module to load	-	No
-V	Print version and exit	-	No

Future Directions

• Job Arrays: Support for generating Slurm job arrays.
• Template Customization: Allow users to provide a custom user-defined template for the .sbatch header.
• Dependency Handling: Logic to chain jobs based on input order.