diff --git a/PTL1/Genomes/Scripts/wrapper_submit.sh b/PTL1/Genomes/Scripts/wrapper_submit.sh index da4cbc5..25d241d 100644 --- a/PTL1/Genomes/Scripts/wrapper_submit.sh +++ b/PTL1/Genomes/Scripts/wrapper_submit.sh @@ -1,24 +1,33 @@ +## Last updated Jan 2025 by Auden Cote-L'Heureux + +## This script is intended to be used to process genomic CDS with EukPhylo part 1 on an HPC that uses the Slurm workload manager. +## The first part of the script are Slurm-specific parameters that should be adjusted by users to fit their resource allocation +## needs and restrictions, followed by some example commands taken from the GitHub Wiki, more detail for which can be found +## here: https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-Part-1:-GF-assignment + + #!/bin/bash -# -#SBATCH --job-name=PTL1_genome -#SBATCH --output=PTL1.%j.out # Stdout (%j expands to jobId) + +## Slurm specific code + +#SBATCH --job-name=EukPhylo +#SBATCH --output=EukPhylo.%j.out # Stdout (%j expands to jobId) #SBATCH --nodes=1 #SBATCH --ntasks=1 -#SBATCH --ntasks-per-node=64 ##change to number of srun when running multiple instances +#SBATCH --ntasks-per-node=64 # #change to number of srun when running multiple instances #SBATCH --mem=160G -#SBATCH --mail-type=ALL -#SBATCH --mail-user=YOUREMAIL@smith.edu module purge #Cleans up any loaded modules -module use /gridapps/modules/all #make sure module locations is loaded - module load slurm module load tqdm module load Biopython/1.75-foss-2019b-Python-3.7.4 module load BLAST+/2.9.0-gompi-2019b module load DIAMOND/0.9.30-GCC-8.3.0 -path='/beegfs/fast/katzlab/PTL1/Genomes/' +path='/Your/Home/Folder' + +## Example run command + +# Start at script 1 and go through script 5 (the final script) using the Universal genetic code +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 -srun -D ${path}Scripts python3 ${path}Scripts/wrapper.py -1 1 -2 5 --cds ${path}PTL1GenomesBatches/PTL1GenomesBatch2 -o ${path}Output/PTL1Genomes_OutputBatch2 --genetic_code Universal --databases ${path}Databases & -wait