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35 lines
1.4 KiB
Bash
35 lines
1.4 KiB
Bash
#!/bin/bash
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## 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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## 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 double number of srun when running multiple instances
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#SBATCH --mem=160G
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#SBATCH --mail-type=ALL
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#SBATCH --mail-user=email@email.edu
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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/4.62.3-GCCcore-11.2.0
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module load Biopython/1.79-foss-2021b
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module load BLAST+/2.12.0-gompi-2021b
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module load DIAMOND/2.0.13-GCC-11.2.0
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module load VSEARCH/2.22.1-GCC-11.3.0
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parent='/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 ${parent}Scripts python3 ${parent}Scripts/wrapper.py -1 1 -2 5 --cds ${parent}Input -o ${parent}Output --genetic_code Universal --databases ${parent}Databases > log.out
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