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Update run_eukphylo.sh

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Adri K. Grow 2025-08-25 17:20:28 -04:00 committed by GitHub
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1 changed files with 3 additions and 3 deletions
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PTL2/run_eukphylo.sh
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@ -9,7 +9,7 @@
## SLURM-SPECIFIC SETUP BELOW ## SLURM-SPECIFIC SETUP BELOW
############# UMass HPC (Unity) requirements below ##################### (DELETE section if not applicable): ############### FOR UMASS UNITY HPC ############### (DELETE section if not applicable):
#SBATCH --job-name=EukPhylo #SBATCH --job-name=EukPhylo
#SBATCH -n 10 # Number of Cores per Task #SBATCH -n 10 # Number of Cores per Task
#SBATCH --mem=125G # Requested Memory #SBATCH --mem=125G # Requested Memory
@ -26,7 +26,7 @@ module load mafft/7.505
module load diamond/2.1.7 module load diamond/2.1.7
conda activate /work/pi_lkatz_smith_edu/Conda_PTL6p2/envs/PTL/ conda activate /work/pi_lkatz_smith_edu/Conda_PTL6p2/envs/PTL/
############# Smith HPC (Grid) requirements below ##################### (DELETE section if not applicable): ############### FOR SMITH GRID HPC ############### (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
@ -49,7 +49,7 @@ 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=$PATH:/beegfs/fast/katzlab/grid_phylotol_setup/programs/standard-RAxML-master #Smith College HPC specific #export PATH=$PATH:/Path/To/Executable/Files
## Provide your parent path ## PROVIDE YOUR PARENT PATH
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)
## EXAMPLE RUN COMMANDS BELOW ## EXAMPLE RUN COMMANDS BELOW