mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-27 06:50:24 +08:00
36 lines
1.7 KiB
Bash
36 lines
1.7 KiB
Bash
#!/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 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
|
|
|
|
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 commands
|
|
|
|
# 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 --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
|