From 094d41cd0d3ae99f70e39f8ffb11eeb7cea3ecf7 Mon Sep 17 00:00:00 2001
From: Natalie Elphick <natalie.elphick@gladstone.ucsf.edu>
Date: Mon, 15 Apr 2024 14:50:14 -0700
Subject: [PATCH] fix typo and missing line in samtools installation
 instructions

---
 docs/Working_on_Wynton_Part_1.html                 | 3 ++-
 working-on-wynton-hpc/Working_on_Wynton_Part_1.Rmd | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/docs/Working_on_Wynton_Part_1.html b/docs/Working_on_Wynton_Part_1.html
index 72c1c0f..320d301 100644
--- a/docs/Working_on_Wynton_Part_1.html
+++ b/docs/Working_on_Wynton_Part_1.html
@@ -672,7 +672,7 @@ application</li>
 Cluster</a></li>
 </ul>
 <p><u>Names</u>:</p>
-<p>log1, log2 and plog (for PHI users)</p>
+<p>log1, log2 and plog1 (for PHI users)</p>
 </section>
 <section id="login" class="slide level2 small-bullets">
 <h2 class="small-bullets">Login</h2>
@@ -1015,6 +1015,7 @@ from source</a></li>
 <li>Create install location and configure</li>
 </ol>
 <pre><code>[alice@dev1 ~]$ mkdir -p $HOME/software/samtools-1.14
+[alice@dev1 ~]$ cd samtools-1.19.2
 [alice@dev1 ~]$ ./configure --prefix=$HOME/software/samtools-1.14</code></pre>
 <ol start="3" type="1">
 <li>Build and install</li>
diff --git a/working-on-wynton-hpc/Working_on_Wynton_Part_1.Rmd b/working-on-wynton-hpc/Working_on_Wynton_Part_1.Rmd
index 8c35b81..2717a15 100644
--- a/working-on-wynton-hpc/Working_on_Wynton_Part_1.Rmd
+++ b/working-on-wynton-hpc/Working_on_Wynton_Part_1.Rmd
@@ -88,7 +88,7 @@ TAs:
 
 <u>Names</u>:
 
-log1, log2 and plog (for PHI users)
+log1, log2 and plog1 (for PHI users)
 
 ## Login {.small-bullets}
 
@@ -335,6 +335,7 @@ echo '[alice@dev1 ~]$ mkdir -p "/scratch/$USER"
 
 ```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
 echo '[alice@dev1 ~]$ mkdir -p $HOME/software/samtools-1.14'
+echo '[alice@dev1 ~]$ cd samtools-1.19.2'
 echo '[alice@dev1 ~]$ ./configure --prefix=$HOME/software/samtools-1.14'
 ```