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Update run_eukphylo.sh

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Adri K. Grow 2025-08-25 17:15:31 -04:00 committed by GitHub
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PTL2/run_eukphylo.sh
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@ -7,22 +7,32 @@
## These run commands can also be copied and run in the terminal / command line separately, without a shell script. ## These run commands can also be copied and run in the terminal / command line separately, without a shell script.
## For the contamination loop, We recommend iterating the sister/subsisters loop multiple times as branches will shift. In contrast, we recommend only running clade grabbing once ## For the contamination loop, We recommend iterating the sister/subsisters loop multiple times as branches will shift. In contrast, we recommend only running clade grabbing once
## SLURM-SPECIFIC SETUP BELOW ## SLURM-SPECIFIC SETUP BELOW
############# UMass HPC (Unity) requirements below ##################### (DELETE section if not applicable):
#SBATCH --job-name=EukPhylo
#SBATCH -n 10 # Number of Cores per Task
#SBATCH --mem=125G # Requested Memory
#SBATCH -p cpu # Partition
#SBATCH -q long # long QOS
#SBATCH -t 334:00:00 # Job time limit
#SBATCH --output=Run_EP.%A_%a.out # Stdout (%j expands to jobId)
#SBATCH --mail-type=ALL
#SBATCH --mail-user=email@email.edu
#SBATCH --array=1-600%50
module purge #Cleans up any loaded modules
module load conda/latest
module load mafft/7.505
module load diamond/2.1.7
conda activate /work/pi_lkatz_smith_edu/Conda_PTL6p2/envs/PTL/
############# Smith HPC (Grid) requirements below ##################### (DELETE section if not applicable):
#SBATCH --job-name=EukPhylo # Job name #SBATCH --job-name=EukPhylo # Job name
#SBATCH --output=Run_EukPhylo.%j.out # Stdout (%j expands to jobId) #SBATCH --output=Run_EukPhylo.%j.out # Stdout (%j expands to jobId)
#SBATCH --nodes=1 #SBATCH --nodes=1
#SBATCH --ntasks=10 ## On the Smith College HPC (Grid), we have to change this to be double the number of task/batches you want to launch #SBATCH --ntasks=10 ## On the Smith College HPC (Grid), we have to change this to be double the number of task/batches you want to launch
#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@email.edu ##add your email address for job updates
## UMass HPC (Unity) requirements below (DELETE section if not applicable):
#SBATCH --mem=125G # Requested Memory
#SBATCH -c 24 # Number of Cores per Task
#SBATCH -q long # Partition
#SBATCH -t 336:00:00 # Job time limit
#Load required modules #Load required modules
module purge #Cleans up any loaded modules module purge #Cleans up any loaded modules
module use /gridapps/modules/all #make sure module locations is loaded module use /gridapps/modules/all #make sure module locations is loaded
@ -37,8 +47,8 @@ module load tqdm/4.64.1-GCCcore-12.2.0
module load Python/3.9.6-GCCcore-11.2.0 module load Python/3.9.6-GCCcore-11.2.0
module load Guidance_mid #Smith College HPC specific module load Guidance_mid #Smith College HPC specific
export PATH=$PATH:/beegfs/fast/katzlab/grid_phylotol_setup/programs/standard-RAxML-master #Smith College HPC specific
#export PATH=$PATH:/Path/To/Executable/Files #export PATH=$PATH:/Path/To/Executable/Files
export PATH=$PATH:/beegfs/fast/katzlab/grid_phylotol_setup/programs/standard-RAxML-master #Smith College HPC specific
parent='/Your/Home/Folder/' # The folder where you are running EukPhylo (this should contain the Scripts and input data folders) parent='/Your/Home/Folder/' # The folder where you are running EukPhylo (this should contain the Scripts and input data folders)