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Generalizing and adding examples to run_eukphylo.sh

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Auden Cote-L'Heureux 2025-01-22 12:28:04 -05:00 committed by GitHub
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PTL2/run_eukphylo.sh
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@ -1,18 +1,23 @@
###GA 11/11/24
###Updated run script to include grid and unity commands.
###The first block of code is specific to the grid. The second block is specific to unity. Pick one and delete the other.
## Last updated Jan 2025 by Auden Cote-L'Heureux
## This shell script is used for running EukPhylo part 2, and includes a general setup for use on an HPC that uses
## the Slurm workload manager. It also includes several example run commands, which correspond to examples explained in more detail in the
## EukPhylo Wiki (https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop).
## These run commands can also be copied and run in the terminal / command line separately, without a shell script.
#!/bin/bash
#SBATCH --job-name=GA1 # Job name
#SBATCH --output=Run_phylotol.%j.out # Stdout (%j expands to jobId)
#SBATCH --mail-type=ALL
#SBATCH --mail-user=youremail@smith.edu ##add your email address
## SLURM-SPECIFIC SETUP BELOW
###Grid start
#SBATCH --job-name=EukPhylo # Job name
#SBATCH --output=Run_EukPhylo.%j.out # Stdout (%j expands to jobId)
#SBATCH --nodes=1
#SBATCH --ntasks=10 ##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 -c 24 # Number of Cores per Task
#SBATCH --mem=125G # Requested Memory
#SBATCH -q long # Partition. Only use this on certain HPCs (e.g., Unity at UMass).
#SBATCH -t 336:00:00 # Job time limit
module purge #Cleans up any loaded modules
module use /gridapps/modules/all #make sure module locations is loaded
@ -25,26 +30,23 @@ module load RAxML
module load IQ-TREE/2.1.2-gompi-2021b
module load tqdm/4.64.1-GCCcore-12.2.0
module load Python/3.9.6-GCCcore-11.2.0
export PATH=$PATH:/beegfs/fast/katzlab/grid_phylotol_setup/programs/standard-RAxML-master
parent='/beegfs/fast/katzlab/' #add your path starting with the name of your folder, should begin with /beegfs/fast/katzlab/
#if you are running batches, you need an srun line for each batch!
srun --exact -n 1 -D ${parent} python3 ${parent}Scripts/eukphylo.py --similarity_filter --sim_cutoff 0.95 --sim_taxa sim_taxa.txt --blacklist GuidanceRemovedSeqs_allConservedRuns_ML_nov_dec_2023.txt --start raw --end trees --gf_list B1_listofOGs.txt --taxon_list taxon_list.txt --data OutgroupR2Gs --output ${parent}Output_folder_B1 > Output_folder_B1.out &
wait
###Grid end
export PATH=$PATH:/Path/To/Executable/Files
parent='/Your/Home/Folder/' # The folder where you are running EukPhylo (this should contain the Scripts and input data folders
## RUN COMMANDS BELOW
# A simple run of part 2, starting from ReadyToGo files and running through tree building
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
# 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)
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
# An example of running just the concatenation step of part 2, starting from trees
srun --exact -n 1 -D ${parent} python eukphylo.py --start trees --concatenate --concat_target_taxa Sr_rh --data Output
# See the Wiki (https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop) for more details!
###Unity start
#SBATCH -c 24 # Number of Cores per Task
#SBATCH --mem=125G # Requested Memory
#SBATCH -q long # Partition
#SBATCH -t 336:00:00 # Job time limit
module purge #Cleans up any loaded modules
module load miniconda/22.11.1-1
module load mafft/7.481
module load conda/latest
conda activate /work/pi_lkatz_smith_edu/Conda_PTL6p2/envs/PTL/
parent='/work/pi_lkatz_smith_edu/' #add your path startin>
#if you are running batches, you need an srun line for each batch!
srun -D ${parent} python3 ${parent}Scripts/eukphylo.py --similarity_filter --sim_cutoff 0.99 ## This line is incomplete
wait
###Unity end