From 0383a3dd997cf53b1fb1e25c0a25c6d78937e658 Mon Sep 17 00:00:00 2001
From: Godwin Ani <aniigodwinn@gmail.com>
Date: Tue, 18 Mar 2025 15:35:28 -0400
Subject: [PATCH] Update wrapper_submit.sh

---
 PTL1/Genomes/Scripts/wrapper_submit.sh | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/PTL1/Genomes/Scripts/wrapper_submit.sh b/PTL1/Genomes/Scripts/wrapper_submit.sh
index 5013539..9f7abbc 100644
--- a/PTL1/Genomes/Scripts/wrapper_submit.sh
+++ b/PTL1/Genomes/Scripts/wrapper_submit.sh
@@ -12,3 +12,17 @@
 # Start at script 1 and go through script 5 (the final script) using the Universal genetic code
 python3 Scripts/wrapper.py -1 1 -2 5 --cds Input -o Output --genetic_code Universal --databases Databases > log.out
 
+parent='/EukPhylo/PTL1/Genomes/Scripts/'
+out_dir='/Output_data'
+in_dir='/Input_data'
+
+## EXAMPLE RUN COMMANDS BELOW
+
+# A simple run of part 1
+python3 ${parent}/wrapper.py \
+    --first_script 1 \
+    --last_script 5 \
+    --cds ${in_dir} \
+    --databases ${parent}Databases \
+    --genetic_code Universal \
+    --output ${out_dir} > Output.out