diff --git a/README.md b/README.md index 6a82603de5120a6d8e5e8cceb310c08afcadb7af..47f8d7a3b80f8800b4fce2c0910687c53fc7f6de 100755 --- a/README.md +++ b/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. ``` diff --git a/V2.1/oda_analysis.sh b/V2.1/oda_analysis.sh index 9e75d5d81e6e86d1766d32eab5abefb52d6dd959..5efed6ed4d3d7eadfa93f01f5c8a56ff180499a9 100755 --- a/V2.1/oda_analysis.sh +++ b/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 diff --git a/V2.1/r_w_packages_4.3.2.sif b/V2.1/r_w_packages_4.3.2.sif new file mode 120000 index 0000000000000000000000000000000000000000..07fee82e707c33a2faca9e598ba0ffe85d2c06aa --- /dev/null +++ b/V2.1/r_w_packages_4.3.2.sif @@ -0,0 +1 @@ +/archive/CRI/shared/Singularity/zzy/r_w_packages_4.3.2.sif \ No newline at end of file diff --git a/V2.1/run_analysis.sh b/V2.1/run_analysis.sh index dae341fc84028478c4da82781eb3292edf70d35e..c2b3bec6ccfe1046d97efa0c2ec5502df42b7f38 100644 --- a/V2.1/run_analysis.sh +++ b/V2.1/run_analysis.sh @@ -1,8 +1,7 @@ #!/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