diff --git a/PTL1/Genomes/Scripts/wrapper_submit.sh b/PTL1/Genomes/Scripts/wrapper_submit.sh index 25d241d..8e0f48e 100644 --- a/PTL1/Genomes/Scripts/wrapper_submit.sh +++ b/PTL1/Genomes/Scripts/wrapper_submit.sh @@ -1,3 +1,4 @@ +#!/bin/bash ## 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. @@ -5,9 +6,6 @@ ## 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 - ## Slurm specific code #SBATCH --job-name=EukPhylo @@ -19,15 +17,16 @@ module purge #Cleans up any loaded modules 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 +module load tqdm/4.62.3-GCCcore-11.2.0 +module load Biopython/1.79-foss-2021b +module load BLAST+/2.12.0-gompi-2021b +module load DIAMOND/2.0.13-GCC-11.2.0 +module load VSEARCH/2.22.1-GCC-11.3.0 -path='/Your/Home/Folder' +parent='/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 ${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