Gdr 2981

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: gDR
 Title: Umbrella package for R packages in the gDR suite
-Version: 1.7.1
-Date: 2025-04-16
+Version: 1.7.2
+Date: 2025-06-11
 Authors@R: c(
     person("Allison", "Vuong", , "vuong.allison@gene.com", role = "aut"),
     person("Bartosz", "Czech", role = "aut",

NEWS.md

@@ -1,5 +1,5 @@
-## gDR 1.7.1 - 2025-04-16
-* synchronize Bioconductor and GitHub versioning
+## gDR 1.7.2 - 2025-06-11
+* update installation instructions
 
 ## gDR 1.5.1 - 2024-11-05
 * synchronize Bioconductor and GitHub versioning

README.md

@@ -5,75 +5,25 @@ The gDR suite offers a full stack solution for processing drug response data. Th
 
 ![Figure 1. The overview of R packages that are available via gDR umbrella package.  ](https://raw.githubusercontent.com/gdrplatform/gDR/main/inst/images/overview.png)  
 
-# Website
-A package website is available under [this link](https://gdrplatform.github.io/gDR/).
-
 # Installation
 
-The easiest way to use functions from gDR package is by using the Docker image. Here is one of the ways to do that. 
-
-1. Generate new personal token 
-Firstly, generate new personal token if you don't have one (go to https://github.com/settings/tokens/new).
-
-2. Clone the gDR repository 
-Then, clone the gDR repository via https (not ssh). Please use the personal token when asked for the password.
-
-```
-git clone https://github.com/gdrplatform/gDR.git
-```
+The easiest way to use functions from gDR package is by using the Bioconductor.
 
-3. [Optional] Save access token into .github_access_token.txt file
-Write your access token as a single line in the file: `rplatform/.github_access_token.txt`. 
+1. Install BiocManager
 
 ```
-cp .github_access_token.txt rplatform/
+install.packages("BiocManager")
 ```
 
-4. Docker build 
-Then build the Docker image.
-```
-bash extras/create_image.sh
-```
+2. Install gDR packages
 
-5. Create 'gdr_rstudio' container with RStudio IDE available at http://localhost:8787 (default credentials are login: `rstudio` and password: `gdr`).
 ```
-bash extras/create_container.sh
+BiocManager::install(c("gDRstyle", "gDRtestData", "gDR"), version = "devel")
 ```
 
-You've just successfully set up the environment for the gDR umbrella package. Please see [gDR vignette](vignettes/gDR.Rmd) for examples of usage.
+You've just successfully set up the environment for the gDR umbrella package. Please see [gDR vignette](https://gdrplatform.github.io/gDR/articles/gDR.html) for examples of usage.
 
 
 # How to contribute
 We are eager to make this tool useful for the community. We welcome any suggestions via GitHub issues, or pull requests for bugfixes/new features. When making pull requests, please first have a look at the style conventions in [gDRstyle](https://gdrplatform.github.io/gDRstyle/style_guide.html).
 
-# Preparing your machine to run gDR images
-1. How to install Docker.
-
-Install Docker on MacOS 
-
-https://docs.docker.com/desktop/install/mac-install/
-
-Install Docker on Windows
-
-https://docs.docker.com/desktop/install/windows-install/
-
-Install Docker on Linux
-
-https://docs.docker.com/desktop/install/linux-install/
-
-2. MacOS troubleshooting (M1/M2)
-```
-Could not connect to the R session on RStudio Server
-Unable to connect to service (1)
-```
-To solve the above problem, please execute the steps below:
-```
-Go to Settings
-```
-```
-Click Features in development
-```
-```
-Select checkbox: Use Rossetta for x86/amd64 emulation on Apple Silicon 
-```
-