From 520494c2b557473051fbec8b36839ef744c0ff18 Mon Sep 17 00:00:00 2001
From: Jean-Philippe Fortin <fortin946@gmail.com>
Date: Tue, 30 Aug 2022 20:42:25 -0700
Subject: [PATCH] Updated readmes

---
 README.Rmd              | 27 ++++++---------------------
 README.md               | 27 ++++++---------------------
 vignettes/crisprBwa.Rmd | 24 ++++++------------------
 3 files changed, 18 insertions(+), 60 deletions(-)

diff --git a/README.Rmd b/README.Rmd
index fa20a27..2f6f686 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -45,35 +45,20 @@ Package was developed and tested on R version 4.2.1.
 
 ## Installation from Bioconductor
 
-`crisprBwa` can be installed from Bioconductor using the following
-commands in a fresh R session:
+`crisprBwa` can be installed from from the Bioconductor devel branch
+using the following commands in a fresh R session:
 
 ```{r, eval=FALSE}
-install.packages("BiocManager")
-BiocManager::install("crisprBwa")
-```
-
-The complete documentation for the package can be found [here](https://bioconductor.org/packages/devel/bioc/manuals/crisprBwa/man/crisprBwa.pdf).
-
-## Installation from GitHub
-
-Alternatively, `crisprBwa` and its dependencies can be installed by typing the
-following commands inside of an R session:
+if (!require("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
 
-```r
-install.packages("devtools")
-library(devtools)
-install_github("crisprVerse/Rbwa")
-install_github("crisprVerse/crisprBase")
-install_github("crisprVerse/crisprBwa")
+BiocManager::install(version="devel")
+BiocManager::install("crisprBwa")
 ```
 
 
 
 
-
-
-
 # Building a bwa index
 
 To use `runBwa` or `runCrisprBwa`, users need to first build a BWA
diff --git a/README.md b/README.md
index 0fbc7da..b5e7fd0 100644
--- a/README.md
+++ b/README.md
@@ -12,8 +12,6 @@ crisprBwa: alignment of gRNA spacer sequences using BWA
     -   <a href="#installation-from-bioconductor"
         id="toc-installation-from-bioconductor">Installation from
         Bioconductor</a>
-    -   <a href="#installation-from-github"
-        id="toc-installation-from-github">Installation from GitHub</a>
 -   <a href="#building-a-bwa-index" id="toc-building-a-bwa-index">Building a
     bwa index</a>
 -   <a href="#alignment-using-runcrisprbwa"
@@ -58,28 +56,15 @@ developed and tested on R version 4.2.1.
 
 ## Installation from Bioconductor
 
-`crisprBwa` can be installed from Bioconductor using the following
-commands in a fresh R session:
+`crisprBwa` can be installed from from the Bioconductor devel branch
+using the following commands in a fresh R session:
 
 ``` r
-install.packages("BiocManager")
-BiocManager::install("crisprBwa")
-```
-
-The complete documentation for the package can be found
-[here](https://bioconductor.org/packages/devel/bioc/manuals/crisprBwa/man/crisprBwa.pdf).
-
-## Installation from GitHub
+if (!require("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
 
-Alternatively, `crisprBwa` and its dependencies can be installed by
-typing the following commands inside of an R session:
-
-``` r
-install.packages("devtools")
-library(devtools)
-install_github("crisprVerse/Rbwa")
-install_github("crisprVerse/crisprBase")
-install_github("crisprVerse/crisprBwa")
+BiocManager::install(version="devel")
+BiocManager::install("crisprBwa")
 ```
 
 # Building a bwa index
diff --git a/vignettes/crisprBwa.Rmd b/vignettes/crisprBwa.Rmd
index 27827b5..dad2979 100644
--- a/vignettes/crisprBwa.Rmd
+++ b/vignettes/crisprBwa.Rmd
@@ -59,27 +59,15 @@ Package was developed and tested on R version 4.2.1.
 
 ## Installation from Bioconductor
 
-`crisprBwa` can be installed from Bioconductor using the following
-commands in a fresh R session:
+`crisprBwa` can be installed from from the Bioconductor devel branch
+using the following commands in a fresh R session:
 
 ```{r, eval=FALSE}
-install.packages("BiocManager")
-BiocManager::install("crisprBwa")
-```
-
-
+if (!require("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
 
-## Installation from GitHub
-
-Alternatively, `crisprBwa` and its dependencies can be installed by typing the
-following commands inside of an R session:
-
-```r
-install.packages("devtools")
-library(devtools)
-install_github("crisprVerse/Rbwa")
-install_github("crisprVerse/crisprBase")
-install_github("crisprVerse/crisprBwa")
+BiocManager::install(version="devel")
+BiocManager::install("crisprBwa")
 ```