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Update wrapper_submit.sh

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Adri K. Grow 2025-08-25 11:42:05 -04:00 committed by GitHub
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PTL1/Transcriptomes/Scripts/wrapper_submit.sh
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@ -6,28 +6,17 @@
## 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
############### FOR SMITH GRID HPC ###############
## 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=1 # #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
#SBATCH --mail-type=ALL #SBATCH --mail-type=ALL
#SBATCH --mail-user=email@xxx.edu ##add your email address for job updates #SBATCH --mail-user=email@xxx.edu ##add your email address for job updates
module purge #Cleans up any loaded modules module purge #Cleans up any loaded modules
#Unity server
module use /gridapps/modules/all
module load conda/latest
conda activate hook_env
module load uri/main
module load diamond/2.1.7
module load VSEARCH/2.22.1-GCC-11.3.0
#Grid server
module load slurm module load slurm
module load tqdm/4.62.3-GCCcore-11.2.0 module load tqdm/4.62.3-GCCcore-11.2.0
module load Biopython/1.79-foss-2021b module load Biopython/1.79-foss-2021b
@ -35,6 +24,24 @@ module load BLAST+/2.12.0-gompi-2021b
module load DIAMOND/2.0.13-GCC-11.2.0 module load DIAMOND/2.0.13-GCC-11.2.0
module load VSEARCH/2.22.1-GCC-11.3.0 module load VSEARCH/2.22.1-GCC-11.3.0
############### FOR UMASS UNITY HPC ###############
## 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=64
#SBATCH --mem=40G
#SBATCH --mail-type=ALL
#SBATCH --mail-user=email@xxx.edu
module purge #Cleans up any loaded modules
module use /gridapps/modules/all
module load conda/latest
conda activate hook_env
module load uri/main
module load diamond/2.1.7
module load VSEARCH/2.22.1-GCC-11.3.0
parent='/Your/Home/Folder/' parent='/Your/Home/Folder/'
## Example commands ## Example commands