From f2701e7f65681aadb82b58815d1b3eb0f54c6eb3 Mon Sep 17 00:00:00 2001
From: Godwin Ani <aniigodwinn@gmail.com>
Date: Mon, 11 Nov 2024 17:01:32 -0500
Subject: [PATCH] Update run_phylotol.sh

---
 PTL2/run_phylotol.sh | 43 ++++++++++++++++++++++++++++++-------------
 1 file changed, 30 insertions(+), 13 deletions(-)

diff --git a/PTL2/run_phylotol.sh b/PTL2/run_phylotol.sh
index c5b6cfe..5338289 100644
--- a/PTL2/run_phylotol.sh
+++ b/PTL2/run_phylotol.sh
@@ -1,33 +1,50 @@
+###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.
+
 #!/bin/bash
-#SBATCH --job-name=meta033 ##change this to a shortened name of your project
+#SBATCH --job-name=GA1 # Job name
 #SBATCH --output=Run_phylotol.%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 --mail-type=ALL
 #SBATCH --mail-user=youremail@smith.edu ##add your email address
 
+
+
+###Grid start
+#SBATCH --nodes=1
+#SBATCH --ntasks=10 ##change this to be double the number of task/batches you want to launch
+
 module purge       #Cleans up any loaded modules
-
 module use /gridapps/modules/all    #make sure module locations is loaded
-
 module load slurm
 module load ETE
 module load Biopython/1.79-foss-2021b
 module load DIAMOND/2.0.13-GCC-11.2.0
 module load MAFFT
-module load BioPerl
 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/Adri/p2PTL/033_meta/B1_meta_033/' #add your path starting with the name of your folder, should begin with /beegfs/fast/katzlab/
-
+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/phylotol.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 &
-srun --exact -n 1 -D ${parent} python3 ${parent}Scripts/phylotol.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 B2_listofOGs.txt --taxon_list taxon_list.txt --data OutgroupR2Gs --output ${parent}Output_folder_B2 > Output_folder_B2.out &
-srun --exact -n 1 -D ${parent} python3 ${parent}Scripts/phylotol.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 B3_listofOGs.txt --taxon_list taxon_list.txt --data OutgroupR2Gs --output ${parent}Output_folder_B3 > Output_folder_B3.out &
-srun --exact -n 1 -D ${parent} python3 ${parent}Scripts/phylotol.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 B4_listofOGs.txt --taxon_list taxon_list.txt --data OutgroupR2Gs --output ${parent}Output_folder_B4 > Output_folder_B4.out &
-srun --exact -n 1 -D ${parent} python3 ${parent}Scripts/phylotol.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 B5_listofOGs.txt --taxon_list taxon_list.txt --data OutgroupR2Gs --output ${parent}Output_folder_B5 > Output_folder_B5.out &
 wait
+###Grid end
+
+
+###Unity start
+#SBATCH -c 24 # Number of Cores per Task
+#SBATCH --mem=125G # Requested Memory
+#SBATCH -p cpu-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/phylotol.py --similarity_filter --sim_cutoff 0.99 -->
+wait
+###Unity start