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34 lines
1.3 KiB
Bash
34 lines
1.3 KiB
Bash
## Last updated Jan 2025 by Auden Cote-L'Heureux
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## This script is intended to be used to process genomic CDS with EukPhylo part 1 on an HPC that uses the Slurm workload manager.
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## The first part of the script are Slurm-specific parameters that should be adjusted by users to fit their resource allocation
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## needs and restrictions, followed by some example commands taken from the GitHub Wiki, more detail for which can be found
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## here: https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-Part-1:-GF-assignment
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#!/bin/bash
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## Slurm specific code
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#SBATCH --job-name=EukPhylo
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#SBATCH --output=EukPhylo.%j.out # Stdout (%j expands to jobId)
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#SBATCH --nodes=1
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#SBATCH --ntasks=1
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#SBATCH --ntasks-per-node=64 # #change to number of srun when running multiple instances
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#SBATCH --mem=160G
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module purge #Cleans up any loaded modules
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module load slurm
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module load tqdm
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module load Biopython/1.75-foss-2019b-Python-3.7.4
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module load BLAST+/2.9.0-gompi-2019b
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module load DIAMOND/0.9.30-GCC-8.3.0
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path='/Your/Home/Folder'
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## Example run command
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# Start at script 1 and go through script 5 (the final script) using the Universal genetic code
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srun -D ${path}Scripts python3 ${path}Scripts/wrapper.py -1 1 -2 5 --cds ${path}Input -o ${path}Output --genetic_code Universal --databases ${path}Databases
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