YuuMJ1997/EukPhylo
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docker wrapper_submit.sh

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PTL1/Transcriptomes/Scripts/wrapper_submit.sh
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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
## 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 ## 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.out python3 Scripts/wrapper.py --first_script 1 --last_script 7 --assembled_transcripts AssembledTranscripts --genetic_code Gcode.txt --databases 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