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Update wrapper_submit.sh

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Adri K. Grow 2025-02-13 18:22:03 -05:00 committed by GitHub
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PTL1/Transcriptomes/Scripts/wrapper_submit.sh
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@ -1,3 +1,4 @@
#!/bin/bash
## Last updated Jan 2025 by Auden Cote-L'Heureux ## 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. ## This script is intended to be used to process genomic CDS with EukPhylo part 1 on an HPC that uses the Slurm workload manager.
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## here: https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-Part-1:-GF-assignment ## here: https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-Part-1:-GF-assignment
#!/bin/bash
## Slurm specific code ## Slurm specific code
#SBATCH --job-name=EukPhylo #SBATCH --job-name=EukPhylo
#SBATCH --output=EukPhylo.%j.out # Stdout (%j expands to jobId) #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=1 # #change to number of srun when running multiple instances
#SBATCH --mem=160G #SBATCH --mem=160G
module purge #Cleans up any loaded modules module purge #Cleans up any loaded modules
@ -30,7 +29,7 @@ parent='/Your/Home/Folder'
## Example commands ## Example commands
# A simple run that goes from script 1 to script 7 (the last script) using the Universal genetic code # 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.txt 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 # 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.txt 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