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Updating header and example runs in wrapper_submit.sh

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Auden Cote-L'Heureux 2025-01-22 12:51:10 -05:00 committed by GitHub
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PTL1/Genomes/Scripts/wrapper_submit.sh
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## 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 #!/bin/bash
#
#SBATCH --job-name=PTL1_genome ## Slurm specific code
#SBATCH --output=PTL1.%j.out # Stdout (%j expands to jobId)
#SBATCH --job-name=EukPhylo
#SBATCH --output=EukPhylo.%j.out # Stdout (%j expands to jobId)
#SBATCH --nodes=1 #SBATCH --nodes=1
#SBATCH --ntasks=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 --mem=160G
#SBATCH --mail-type=ALL
#SBATCH --mail-user=YOUREMAIL@smith.edu
module purge #Cleans up any loaded modules module purge #Cleans up any loaded modules
module use /gridapps/modules/all #make sure module locations is loaded
module load slurm module load slurm
module load tqdm module load tqdm
module load Biopython/1.75-foss-2019b-Python-3.7.4 module load Biopython/1.75-foss-2019b-Python-3.7.4
module load BLAST+/2.9.0-gompi-2019b module load BLAST+/2.9.0-gompi-2019b
module load DIAMOND/0.9.30-GCC-8.3.0 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