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docker wrapper_submit.sh

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PTL1/Genomes/Scripts/wrapper_submit.sh
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## needs and restrictions, followed by some example commands taken from the GitHub Wiki, more detail for which can be found ## 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 ## here: https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-Part-1:-GF-assignment
## 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 --mem=160G
module purge #Cleans up any loaded modules
module load slurm
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
parent='/Your/Home/Folder'
## Example run command ## Example run command
# Start at script 1 and go through script 5 (the final script) using the Universal genetic code # Start at script 1 and go through script 5 (the final script) using the Universal genetic code
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 python3 Scripts/wrapper.py -1 1 -2 5 --cds Input -o Output --genetic_code Universal --databases Databases > log.out