09032024

README.md

@@ -22,7 +22,7 @@ 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/oda.sh  /input_path/your_data_file.xlsx  /output_path/  optional_BioHPC_queue_name
+sh  /path_to_the_program/oda_analysis.sh  /input_path/your_data_file.xlsx  /output_path/  optional_BioHPC_queue_name
 ```
 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.
 ```

V2.1/oda_analysis.sh

@@ -3,13 +3,13 @@ if [[ $# < 2 ]]
 then
 	echo "########## ODA Tool Usage ##########"
 	echo "If you are a BioHPC user at UTSW, run the following command from a BioHPC terminal:"
-	echo "sh script_path/run_analysis.sh (this file) input_path/input_file_name.xlsx output_path optional_BioHPC_queue_name"
+	echo "sh script_path/oda_analysis.sh (this file) input_path/input_file_name.xlsx output_path optional_BioHPC_queue_name"
 	echo
-	echo "If you are not a BioHPC user and have installed R locally, run the following command from your computer's terminal/shell:"
+	echo "If you are not a BioHPC user and have installed R locally, run the following command from your computer's terminal/shell with Singularity:"
 	echo "Rscript script_path/ODA.R input_path/input_file_name.xlsx output_path"
 	echo
-	echo "Alternatively, you can run the following command if you have bash for the local terminal/shell:"
-	echo "sh script_path/run_analysis.sh (this file) input_path/input_file_name.xlsx output_path local"
+	echo "Alternatively, you can run the following command if you have bash for the local terminal/shell with Singularity:"
+	echo "sh script_path/oda_analysis.sh (this file) input_path/input_file_name.xlsx output_path local"
 	echo "########## ODA Tool Usage ##########"
 	exit
 fi

V2.1/r_w_packages_4.3.2.sif

+/archive/CRI/shared/Singularity/zzy/r_w_packages_4.3.2.sif
\ No newline at end of file

V2.1/run_analysis.sh

 #!/bin/bash
-#module load R/4.0.2-gccmkl	#Comment this line out (adding a # at the beginning) if running from your own computer.
 module load singularity/3.9.9
-ODA_MODULE=/archive/CRI/shared/Singularity/zzy/r_w_packages_4.3.2.sif
 ODA_DIR=$1
+ODA_MODULE=	$ODA_DIR/r_w_packages_4.3.2.sif	#Link to: /archive/CRI/shared/Singularity/zzy/r_w_packages_4.3.2.sif
 INPUT_FILE=$2
 OUTPUT_FOLDER=$3
 singularity exec $ODA_MODULE Rscript $ODA_DIR/ODA/ODA.R $INPUT_FILE $OUTPUT_FOLDER 2>&1 | tee -a $OUTPUT_FOLDER/ODA_run.log