From 2247fd026e5559a0ccc6b804ff16d6a227f459fc Mon Sep 17 00:00:00 2001
From: yilinxu <yellen10@gmail.com>
Date: Sun, 17 Jan 2021 17:10:28 -0600
Subject: [PATCH 1/3] Update README.md

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

diff --git a/README.md b/README.md
index 8399d02..1d03221 100644
--- a/README.md
+++ b/README.md
@@ -25,5 +25,8 @@ python setup.py develop
 ## Run shell script
 ```
 cd gen3-augur
+mkdir data
+mkdir logs
+mkdir results
 bash gen3-augur.sh >> logs/run_pipeline.log
 ```

From 797497de9e25a2d8ea55a31c93ac518dcaaf0e2e Mon Sep 17 00:00:00 2001
From: yilinxu <yellen10@gmail.com>
Date: Sun, 17 Jan 2021 17:12:00 -0600
Subject: [PATCH 2/3] Update README.md

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 1d03221..3703aff 100644
--- a/README.md
+++ b/README.md
@@ -28,5 +28,6 @@ cd gen3-augur
 mkdir data
 mkdir logs
 mkdir results
+mkdir auspice
 bash gen3-augur.sh >> logs/run_pipeline.log
 ```

From 8c6f8797e1fe2f71384f02b6eac9c329a63c86d2 Mon Sep 17 00:00:00 2001
From: yilinxu <yellen10@gmail.com>
Date: Sun, 17 Jan 2021 17:13:06 -0600
Subject: [PATCH 3/3] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 3703aff..ea6b575 100644
--- a/README.md
+++ b/README.md
@@ -3,7 +3,7 @@ Access complete genomic sequence from gen3 data common https://chicagoland.pande
 
 ## Download credentials.json from data common and copy the credentials.json into config folder
 ```
-copy credentials.json gen3-augur/config
+copy credentials.json gen3-augur/config/credentials.json
 ```
 
 ## Installing dependencies