From c4b100e05b0a2ee0943d6da594088a0e1ffb5fc3 Mon Sep 17 00:00:00 2001
From: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Thu, 7 Nov 2024 17:35:34 -0800
Subject: [PATCH] Update README.md

Added R_LIB_USER folder creation and SINGULARITY_CACHEDIR setting
---
 .../Workflow_Documentation/GL_RefAnnotTable-A/README.md    | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/GeneLab_Reference_Annotations/Workflow_Documentation/GL_RefAnnotTable-A/README.md b/GeneLab_Reference_Annotations/Workflow_Documentation/GL_RefAnnotTable-A/README.md
index 9bfea792..44e5de46 100644
--- a/GeneLab_Reference_Annotations/Workflow_Documentation/GL_RefAnnotTable-A/README.md
+++ b/GeneLab_Reference_Annotations/Workflow_Documentation/GL_RefAnnotTable-A/README.md
@@ -96,7 +96,7 @@ Once complete, a `singularity` folder containing the Singularity images will be
 # Set R library path to current working directory
 export R_LIBS_USER=$(pwd)/R_libs
 # Create the specified R library path if it doesn't already exist
-mkdir -p $R_LIBS
+mkdir -p $R_LIBS_USER
 
 # Set Singularity cache directory 
 export SINGULARITY_CACHEDIR=$(pwd)/singularity
@@ -217,6 +217,11 @@ If the reference table does not specify an annotations database for the target o
 ```bash
 # Set R library path if not already set
 export R_LIBS_USER=$(pwd)/R_libs
+# Create the specified R library path if it doesn't already exist
+mkdir -p $R_LIBS_USER
+
+# Set Singularity cache directory if not already set
+export SINGULARITY_CACHEDIR=$(pwd)/singularity
 
 singularity exec \
     --bind $(pwd):$(pwd) \