From 68551d76ccd0de742459340a3cea3841aedd1b16 Mon Sep 17 00:00:00 2001
From: Zhiyu <zhiyu.zhao@utsouthwestern.edu>
Date: Wed, 1 May 2024 22:17:00 -0500
Subject: [PATCH] 05012024

---
 README.md | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 2e506db..de620e9 100755
--- a/README.md
+++ b/README.md
@@ -22,11 +22,15 @@ This is an R program to visualize and analyze -omics data such as those from mic
 
 1. Running on the BioHPC @ UTSW. Log on the BioHPC ***Portal***, launch a ***Web Visualization*** node, open a terminal from there, and run the following:
 ```
-sh  /path_to_the_program/run_analysis.sh  /input_path/your_data_file.xlsx  /output_path/your_result_file.xlsx  optional_BioHPC_queue_name
+sh  /path_to_the_program/oda.sh  /input_path/your_data_file.xlsx  /output_path/  optional_BioHPC_queue_name
 ```
-2. Running on your local machine. Make sure R is installed and you can run the Rscript command from a command line tool such as a Linux terminal or Windows CMD / PowerShell.
+2. Running on your local machine with a Singularity / Docker / Podman container. Make sure Singularity / Docker / Podman is installed and you can run it from a command line tool such as a Linux terminal or Windows CMD / PowerShell. You should request a copy of the corresponding container from me.
 ```
-Rscript  /path_to_the_program/ODA.R  /input_path/your_data_file.xlsx  /output_path/your_result_file.xlsx
+singularity exec oda_container Rscript /path_to_the_program/ODA.R  /input_path/your_data_file.xlsx  /output_path/
+```
+3. Running on your local machine. Make sure R and required packages are installed and you can run the Rscript command from a command line tool such as a Linux terminal or Windows CMD / PowerShell.
+```
+Rscript  /path_to_the_program/ODA.R  /input_path/your_data_file.xlsx  /output_path/
 ```
 
 ## Examples: See the Examples folder for typical analysis settings and output files (more to be added).
-- 
GitLab