From 88c166754aaf0bdd345766935e22691f29a8d797 Mon Sep 17 00:00:00 2001 From: Godwin Ani Date: Mon, 24 Feb 2025 11:28:38 -0500 Subject: [PATCH] docker wrapper_submit.sh --- PTL1/Transcriptomes/Scripts/wrapper_submit.sh | 22 +------------------ 1 file changed, 1 insertion(+), 21 deletions(-) diff --git a/PTL1/Transcriptomes/Scripts/wrapper_submit.sh b/PTL1/Transcriptomes/Scripts/wrapper_submit.sh index cdc9424..32e89f3 100644 --- a/PTL1/Transcriptomes/Scripts/wrapper_submit.sh +++ b/PTL1/Transcriptomes/Scripts/wrapper_submit.sh @@ -7,29 +7,9 @@ ## 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 +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