#!/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.
## 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

## SLURM-SPECIFIC SETUP BELOW

############### FOR SMITH GRID HPC ############### (DELETE section if not applicable):
## 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=1 ##change to number of srun when running multiple instances
#SBATCH --mem=160G
#SBATCH --mail-type=ALL
#SBATCH --mail-user=email@xxx.edu ##add your email address for job updates
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

############### FOR UMASS UNITY HPC ############### (DELETE section if not applicable):
## 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
#SBATCH --mem=40G
#SBATCH --mail-type=ALL
#SBATCH --mail-user=email@xxx.edu
module purge       #Cleans up any loaded modules
module use /gridapps/modules/all
module load conda/latest
module load uri/main
module load diamond/2.1.7
module load VSEARCH/2.22.1-GCC-11.3.0
conda activate /work/pi_lkatz_smith_edu/Conda_PTL6p1

## PROVIDE YOUR PARENT PATH
parent='/Your/Home/Folder/'

## EXAMPLE RUN COMMANDS BELOW

# A simple run that goes from script 1 to script 7 (the last script) using the Universal genetic code
srun -D ${parent}Scripts python3 ${parent}Scripts/wrapper.py --first_script 1 --last_script 7 --assembled_transcripts ${parent}AssembledTranscripts -o ${parent}Out --genetic_code ${parent}Gcode.txt --databases ${parent}Databases > log.out

# Including the cross-plate contamination step, using conspecific names
srun -D ${parent} python3 ${parent}Scripts/wrapper.py --first_script 1 --last_script 7 --assembled_transcripts ${parent}AssembledTranscripts --output . --genetic_code ${parent}Gcode.txt --databases ${parent}Databases --xplate_contam --conspecific_names ${parent}Conspecific.txt > log.out