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waldronlab · Aug 5, 2021 · b93f3cf · b93f3cf
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diff --git a/vignettes/hands-on.Rmd b/vignettes/hands-on.Rmd
@@ -28,7 +28,7 @@ This workspace performs bulk RNASeq differential expression from FASTQ files.
 Salmon quantification step is implemented in WORKFLOWS and the downstream 
 analysis by DESeq2 is available under NOTEBOOKS.
 
-1. Login to Terra and navigate to **"Bioconductor-Workflow-DESeq2"** workspace  
+1. Login to Terra and navigate to **"Bioconductor-Workflow-DESeq2-BioC2021"** workspace  
 2. Clone this workspace:    
 - Assign a *unique* workspace name   
 - Use the billing project, **"bioc2021-workshop"**   

diff --git a/vignettes/images/clone_demo_workspace2.png b/vignettes/images/clone_demo_workspace2.png
diff --git a/vignettes/live-demo.Rmd b/vignettes/live-demo.Rmd
@@ -27,7 +27,7 @@ If necessary, install the AnVILPublish library.
 
 ```{r message=FALSE, eval=FALSE}
 if (!"AnVILPublish" %in% rownames(installed.packages()))
-    BiocManager::install("AnVILPublish")
+    AnVIL::install("AnVILPublish")
 ```
 
 There are only a small number of functions in the package; it is
@@ -60,10 +60,6 @@ Note that these be used to set, as well as interrogate, the account and project.
 Conversion of .Rmd vignettes to .ipynb notebooks uses [notedown](https://github.com/aaren/notedown)
 python software. It must be available from within _R_, e.g.,
 
-```{r echo=FALSE, eval=FALSE}
-Sys.setenv(PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/rstudio/.local/bin")
-```
-
 ```{r}
 system2("notedown", "--version")
 ```

diff --git a/vignettes/overview.Rmd b/vignettes/overview.Rmd
@@ -140,17 +140,19 @@ This section also includes links to other helpful open source workflow repositor
 
 ![](images/code_workflows.png)
 
+<br>
+
 # Examples for today's workshop
 In this workshop, we will introduce multiple examples demonstrating what you
 can do using Terra. 
 
 |Session | Example | Where | Objective |
 |---|---|---|---|
 |Usecase|CNV analysis|Terra|Reproducibility + Storage/Compute|
-||Teaching|Terra|Convenient setup|
+||Teaching|Terra|Convenient setup + Collaboration|
 |Live demo|AnVILPublish|Your laptop --> Terra|Reproducibility|
 ||GenomicSuperSignature|Terra RStudio|Convenient setup + Reproducibility|
 ||RunTerraWorkflow (beta)|Your laptop|Remote use of Terra|
-|Hands-on|DESeq2|Terra|Demonstrate Terra Structure|
+|Hands-on|DESeq2|Terra|Demonstrate Terra|