Merge pull request #55 from ccb-hms/upd_install

condense package list, remove R/RStudio instructions, refer to bioc-i…
carpentries-incubator · Oct 7, 2024 · bc00eae · bc00eae
2 parents d87f1f0 + 8f633b8
commit bc00eae
Showing 1 changed file with 8 additions and 137 deletions.
diff --git a/learners/setup.md b/learners/setup.md
@@ -7,120 +7,9 @@ title: Setup
 ### R and RStudio
 
 - R and RStudio are separate downloads and installations. R is a programming language and collection of software that implements that language. RStudio is a graphical integrated development environment
-(IDE) that makes using R much easier and more interactive. You need to install R
+(IDE) that makes using R easier and more interactive. You need to install R
 before you install RStudio. After installing both programs, you will need to
-install some R libraries from within RStudio. Follow the instructions below for
-your operating system, and then follow the instructions to install packages.
-
-### You are running Windows
-
-<br>
-
-:::::::::::::::  solution
-
-## If you already have R and RStudio installed
-
-- Open RStudio, and click on "Help" > "Check for updates". If a new version is
-  available, quit RStudio, and download the latest version for RStudio.
-- To check which version of R you are using, start RStudio and the first thing
-  that appears in the console indicates the version of R you are
-  running. Alternatively, you can type `sessionInfo()`, which will also display
-  which version of R you are running. Go on
-  the [CRAN website](https://cran.r-project.org/bin/windows/base/) and check
-  whether a more recent version is available. If so, please download and install
-  it. You can [check here](https://cran.r-project.org/bin/windows/base/rw-FAQ.html#How-do-I-UNinstall-R_003f) for
-  more information on how to remove old versions from your system if you wish to do so.
-- Follow the steps in the instructions [for everyone](#for-everyone) at the
-  bottom of this page.
-
-
-:::::::::::::::::::::::::
-
-:::::::::::::::  solution
-
-## If you don't have R and RStudio installed
-
-- Download R from
-  the [CRAN website](https://cran.r-project.org/bin/windows/base/release.htm).
-- Run the `.exe` file that was just downloaded
-- Go to the [RStudio download page](https://www.rstudio.com/products/rstudio/download/#download)
-- Under *All Installers* select **RStudio xxxx.yy.zz-uuu.exe - Windows 10/11** (where x, y, z, and u represent version numbers)
-- Double click the file to install it
-- Once it's installed, open RStudio to make sure it works and you don't get any
-  error messages
-- Follow the steps in the instructions [for everyone](#for-everyone) at the
-  bottom of this page.
-
-:::::::::::::::::::::::::
-
-### You are running macOS
-
-<br>
-
-:::::::::::::::  solution
-
-## If you already have R and RStudio installed
-
-- Open RStudio, and click on "Help" > "Check for updates". If a new version is
-  available, quit RStudio, and download the latest version for RStudio.
-- To check the version of R you are using, start RStudio and the first thing
-  that appears on the terminal indicates the version of R you are running. Alternatively, you can type `sessionInfo()`, which will
-  also display which version of R you are running. Go on
-  the [CRAN website](https://cran.r-project.org/bin/macosx/) and check
-  whether a more recent version is available. If so, please download and install
-  it.
-- Follow the steps in the instructions [for everyone](#for-everyone) at the
-  bottom of this page.
-
-
-:::::::::::::::::::::::::
-
-:::::::::::::::  solution
-
-## If you don't have R and RStudio installed
-
-- Download R from
-  the [CRAN website](https://cran.r-project.org/bin/macosx/).
-- Select the `.pkg` file for the latest R version
-- Double click on the downloaded file to install R
-- It is also a good idea to install [XQuartz](https://www.xquartz.org/) (needed
-  by some packages)
-- Go to the [RStudio download page](https://www.rstudio.com/products/rstudio/download/#download)
-- Under *All Installers* select **RStudio xxxx.yy.zz-uuu.dmg - macOS 10.15+** (where x, y, z, and u represent version numbers)
-- Double click the file to install RStudio
-- Once it's installed, open RStudio to make sure it works and you don't get any
-  error messages.
-- Follow the steps in the instructions [for everyone](#for-everyone) at the
-  bottom of this page.
-
-
-:::::::::::::::::::::::::
-
-### You are running Linux
-
-<br>
-
-:::::::::::::::  solution
-
-## Install R using your package manager and RStudio
-
-- Follow the instructions for your distribution
-  from [CRAN](https://cloud.r-project.org/bin/linux), they provide information
-  to get the most recent version of R for common distributions. For most
-  distributions, you could use your package manager (e.g., for Debian/Ubuntu run
-  `sudo apt-get install r-base`, and for Fedora `sudo yum install R`), but we
-  don't recommend this approach as the versions provided by this are
-  usually out of date. In any case, make sure you have at least R 4.2.0.
-- Go to the [RStudio download
-  page](https://www.rstudio.com/products/rstudio/download/#download)
-- Under *All Installers* select the version that matches your distribution, and
-  install it with your preferred method (e.g., with Debian/Ubuntu `sudo dpkg -i rstudio-xxxx.yy.zz-uuu-amd64.deb` at the terminal).
-- Once it's installed, open RStudio to make sure it works and you don't get any
-  error messages.
-- Follow the steps in the [instructions for everyone](#for-everyone)
-
-
-:::::::::::::::::::::::::
+install some R libraries from within RStudio. If you need to install R and/or RStudio, there are platform-specific installation instructions in the [Introduction to Bioconductor module](https://carpentries-incubator.github.io/bioc-intro/).
 
 ### For everyone
 
@@ -132,37 +21,19 @@ double-clicking the icon and enter these commands:
 ```r
 install.packages(c("BiocManager", "remotes"))
 
-BiocManager::install(c("AUCell", "batchelor", "BiocNeighbors", 
-                       "BiocParallel", "BiocSingular", "BiocStyle", 
-                       "bluster", "CuratedAtlasQueryR", "dplyr", 
-                       "DropletUtils", "edgeR", "EnsDb.Mmusculus.v79", 
-                       "ggplot2", "GSEABase", "MouseGastrulationData",
-                       "pheatmap", "scater", "scDblFinder", "scran", 
-                       "scuttle", "Seurat", "SeuratData", 
-                       "SingleCellExperiment", "SingleR",
-                       "TENxBrainData", "zellkonverter"),
+BiocManager::install(c("AUCell", "batchelor", "BiocStyle", 
+                       "CuratedAtlasQueryR", "DropletUtils", 
+                       "EnsDb.Mmusculus.v79", "MouseGastrulationData",
+                       "scDblFinder", "Seurat", "lgeistlinger/SeuratData",
+                       "SingleR", "TENxBrainData", "zellkonverter"),
                        Ncpus = 4)
 ```
 
 <!--- 
 grep -Ph "library\(" episodes/*.Rmd | sort | uniq 
 
-^these are all libraries used in the episodes
+^these are all libraries loaded in the episodes
 -->
 
-On the off chance your computer don't have multiple CPU cores, remove the `Ncpus
-= 4` argument.
-
-If you've worked with Bioconductor packages before, and the installation command
-offers to update packages that have newer versions, saying something like:
-
-```
-<...long list of packages...>
-
-Update all/some/none? [a/s/n]:
-```
-
-Select `n` for no. If old packages turn out to be a problem, cross that bridge
-when you come to it.