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https://github.com/baerlachlan/smk-cluster-generic-slurm

Snakemake profile for Slurm execution via the cluster-generic plugin

https://github.com/baerlachlan/smk-cluster-generic-slurm

Science Score: 13.0%

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Repository

Snakemake profile for Slurm execution via the cluster-generic plugin

Basic Info
  • Host: GitHub
  • Owner: baerlachlan
  • Language: Shell
  • Default Branch: main
  • Homepage:
  • Size: 6.84 KB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 2 years ago · Last pushed over 1 year ago
Metadata Files
Readme

README.md

Snakemake profile for Slurm execution

My personal config for slurm execution of snakemake workflows.

Requires Snakemake minimum version 8.

This setup originated from John Blischak's smk-simple-slurm, but has been modified over several years and Snakemake versions.

Installation

If snakemake is not already installed on your system, install it via Conda:

bash conda create -c conda-forge -c bioconda -n snakemake snakemake

Install the cluster-generic plugin inside your the Snakemake environment:

bash conda activate snakemake conda install snakemake-executor-plugin-cluster-generic

Profile setup

Add the profile to your user configuration directory:

bash mkdir -p ~/.config/snakemake cd ~/.config/snakemake git clone git@github.com:baerlachlan/smk-cluster-generic-slurm.git

Modify the account and partition parameters to the sbatch command in config.v8+.yaml under the cluster-generic-submit-cmd option.

Also modify the wrapper-prefix option if you intend to use snakemake wrappers stored locally. This is my strategy for using wrappers on compute nodes with no internet.

Usage

Pass the folder name when executing Snakemake:

bash snakemake --profile smk-cluster-generic-slurm

Optionally, set the default profile in your ~/.bashrc and omit the --profile argument:

bash echo "export SNAKEMAKE_PROFILE=smk-cluster-generic-slurm" >> ~/.bashrc snakemake

Owner

  • Name: Lachlan Baer
  • Login: baerlachlan
  • Kind: user
  • Location: Adelaide, South Australia
  • Company: University of Adelaide

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