From 616a05348d55a5cd7d4ec95d61efff6f1d6cd2c5 Mon Sep 17 00:00:00 2001
From: Godwin Ani <aniigodwinn@gmail.com>
Date: Fri, 14 Mar 2025 15:02:49 -0400
Subject: [PATCH] Updated Home (markdown)

---
 Home.md | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/Home.md b/Home.md
index 61ffd2d..dd84bf1 100644
--- a/Home.md
+++ b/Home.md
@@ -13,13 +13,24 @@ We are in the process of containerizing EukPhylo with Docker, and we have starte
 
 ```bash
 # Build the container
-docker build -f Dockerfile.txt . --tag eukphylo:1
+docker build -f Dockerfile.txt . --tag eukphylo
+
 
 # Current command is:
 docker run -it \
+    --mount type=bind,src=$(pwd)/databases,dst=/Databases \
     --mount type=bind,src=$(pwd)/input_data,dst=/Input_data \
     --mount type=bind,src=$(pwd)/output_data,dst=/Output_data \
-    eukphylo:1
+    eukphylo
+```
+An example for running the dockerfile that takes in an OGlist, taxonlist, and R2Gs as input. It also requires an Output folder.
+```
+docker run -it \
+--mount type=bind,src=/Users/gani/phylotol_ms/Docker/PT2/PTL2listofOGs.txt,dst=/EukPhylo/PTL2listofOGs.txt \
+--mount type=bind,src=/Users/gani/phylotol_ms/Docker/PT2/taxon_list.txt,dst=/EukPhylo/PTL2taxon_list.txt \
+--mount type=bind,src=/Users/gani/phylotol_ms/Docker/PT2/R2G,dst=/Input_data \
+--mount type=bind,src=/Users/gani/phylotol_ms/Docker/PT2/Output_data,dst=/Output_data \
+eukphylo
 ```
 
 After development, GitHub CICD workflows can be added to automatically build and release the dockerfile for the end user.