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53 lines
2.7 KiB
Bash
53 lines
2.7 KiB
Bash
## Last updated Jan 2025 by Auden Cote-L'Heureux
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## This shell script is used for running EukPhylo part 2, and includes a general setup for use on an HPC that uses
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## the Slurm workload manager. It also includes several example run commands, which correspond to examples explained in more detail in the
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## EukPhylo Wiki (https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop).
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## These run commands can also be copied and run in the terminal / command line separately, without a shell script.
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#!/bin/bash
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## SLURM-SPECIFIC SETUP BELOW
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#SBATCH --job-name=EukPhylo # Job name
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#SBATCH --output=Run_EukPhylo.%j.out # Stdout (%j expands to jobId)
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#SBATCH --nodes=1
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#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
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#SBATCH -c 24 # Number of Cores per Task
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#SBATCH --mem=125G # Requested Memory
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#SBATCH -q long # Partition. Only use this on certain HPCs (e.g., Unity at UMass).
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#SBATCH -t 336:00:00 # Job time limit
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module purge #Cleans up any loaded modules
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module use /gridapps/modules/all #make sure module locations is loaded
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module load slurm
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module load ETE
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module load Biopython/1.79-foss-2021b
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module load DIAMOND/2.0.13-GCC-11.2.0
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module load MAFFT
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module load RAxML
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module load IQ-TREE/2.1.2-gompi-2021b
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module load tqdm/4.64.1-GCCcore-12.2.0
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module load Python/3.9.6-GCCcore-11.2.0
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export PATH=$PATH:/Path/To/Executable/Files
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parent='/Your/Home/Folder/' # The folder where you are running EukPhylo (this should contain the Scripts and input data folders
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## RUN COMMANDS BELOW
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# A simple run of part 2, starting from ReadyToGo files and running through tree building
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srun --exact -n 1 -D ${parent} python3 ${parent}Scripts/eukphylo.py --start raw --end trees --gf_list ${parent}listofOGs.txt --taxon_list ${parent}taxon_list.txt --data ${parent}Input_folder --output ${parent}Output_folder
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# Another example run starting from ReadyToGo files and running through tree building, with the commonly used similarity filter cutoff, blacklist, and "sim_taxa_list" arguments (see Wiki)
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srun --exact -n 1 -D ${parent} python3 ${parent}Scripts/eukphylo.py --start raw --end trees --gf_list ${parent}listofOGs.txt --taxon_list ${parent}taxon_list.txt --data ${parent}Input_folder --output ${parent}Output_folder --similarity_filter --blacklist ${parent}Blacklist.txt --sim_cutoff 0.99 --sim_taxa sim_taxa_list.txt
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# An example of running just the concatenation step of part 2, starting from trees
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srun --exact -n 1 -D ${parent} python eukphylo.py --start trees --concatenate --concat_target_taxa Sr_rh --data Output
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# See the Wiki (https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop) for more details!
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