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Update wrapper_submit.sh

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Adri K. Grow 2025-08-25 17:21:34 -04:00 committed by GitHub
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PTL1/Transcriptomes/Scripts/wrapper_submit.sh
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@ -6,6 +6,8 @@
## 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 SETUP BELOW
############### FOR SMITH GRID HPC ############### (DELETE section if not applicable): ############### FOR SMITH GRID HPC ############### (DELETE section if not applicable):
## Slurm specific code ## Slurm specific code
#SBATCH --job-name=EukPhylo #SBATCH --job-name=EukPhylo
@ -42,9 +44,10 @@ module load diamond/2.1.7
module load VSEARCH/2.22.1-GCC-11.3.0 module load VSEARCH/2.22.1-GCC-11.3.0
conda activate /work/pi_lkatz_smith_edu/Conda_PTL6p1 conda activate /work/pi_lkatz_smith_edu/Conda_PTL6p1
## PROVIDE YOUR PARENT PATH
parent='/Your/Home/Folder/' parent='/Your/Home/Folder/'
## Example commands ## EXAMPLE RUN COMMANDS BELOW
# 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 -o ${parent}Out --genetic_code ${parent}Gcode.txt --databases ${parent}Databases > log.out 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