From 05ecacf9b933022b25df6052eee5b823427622f8 Mon Sep 17 00:00:00 2001
From: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com>
Date: Tue, 25 Feb 2025 10:15:05 +0000
Subject: [PATCH] Update run_eukphylo.sh

Added in the variables to the script to increase configurability.
---
 PTL2/run_eukphylo.sh | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/PTL2/run_eukphylo.sh b/PTL2/run_eukphylo.sh
index 6db85bd..4a3c1b5 100644
--- a/PTL2/run_eukphylo.sh
+++ b/PTL2/run_eukphylo.sh
@@ -6,10 +6,17 @@
 ## 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.
 
-
+parent='/PhyloToL-6/PTL2'
+out_dir='/Output_data'
+in_dir='/Input_data'
 
 ## EXAMPLE RUN COMMANDS BELOW
 
 # A simple run of part 2, starting from ReadyToGo files and running through tree building
-python3 Scripts/eukphylo.py --start raw --end trees --gf_list listofOGs.txt --taxon_list taxon_list.txt --data Input_folder --output Output_folder > Output.out
-
+python3 ${parent}Scripts/eukphylo.py \
+    --start raw \
+    --end trees \
+    --gf_list ${parent}listofOGs.txt \
+    --taxon_list ${parent}taxon_list.txt \
+    --data ${in_dir} \
+    --output ${out_dir} > Output.out