From c1b955d9b26141c56b674789f1e043ab2cb7abcd Mon Sep 17 00:00:00 2001
From: "Adri K. Grow" <42044618+adriannagrow@users.noreply.github.com>
Date: Wed, 30 Aug 2023 09:32:26 -0400
Subject: [PATCH] Add files via upload

---
 PTL2/run_phylotol.sh | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 PTL2/run_phylotol.sh

diff --git a/PTL2/run_phylotol.sh b/PTL2/run_phylotol.sh
new file mode 100644
index 0000000..e9e0bb6
--- /dev/null
+++ b/PTL2/run_phylotol.sh
@@ -0,0 +1,33 @@
+#!/bin/bash
+#SBATCH --job-name=YOUR_PROJECT_NAME ##change this to a shortened name of your project
+#SBATCH --output=Run_phylotol.%j.out # Stdout (%j expands to jobId)
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --ntasks-per-node=4 ##change to number of srun when running multiple instances
+#SBATCH --mem=150G
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=email@smith.edu ##add your email address
+
+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
+module load DIAMOND/0.9.30-GCC-8.3.0
+module load MAFFT
+module load BioPerl
+module load RAxML
+module load IQ-TREE/2.1.2-foss-2020a
+export PATH=$PATH:/beegfs/fast/katzlab/grid_phylotol_setup/programs/standard-RAxML-master
+
+parent='/beegfs/fast/katzlab/<fill in with your path>/' #do not edit this line before katzlab/, add your path starting with the name of your folder
+
+#if you are running batches, you need an srun line for each batch!
+srun -D ${parent} python3 ${parent}Scripts/phylotol.py --start raw --end trees --gf_list listofOGs.txt --taxon_list taxon_list.txt --data OutgroupR2Gs --output ${parent}Output_folder > Output_folder.out &
+#srun -D ${parent} python3 ${parent}Scripts/phylotol.py --start raw --end trees --gf_list mei_batch2.txt --taxon_list taxon_list.txt --data OutgroupR2Gs --output ${parent}mei_output2 > mei_output2.out &
+#srun -D ${parent} python3 ${parent}Scripts/phylotol.py --start raw --end trees --gf_list mei_batch3.txt --taxon_list taxon_list.txt --data OutgroupR2Gs --output ${parent}mei_output3 > mei_output3.out &
+#srun -D ${parent} python3 ${parent}Scripts/phylotol.py --start raw --end trees --gf_list mei_batch4.txt --taxon_list taxon_list.txt --data OutgroupR2Gs --output ${parent}mei_output4 > mei_output4.out &
+
+wait