diff --git a/DESCRIPTION b/DESCRIPTION index 790ef69..722b8f8 100644 --- a/DESCRIPTION +++ b/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", diff --git a/NEWS.md b/NEWS.md index e34702b..05108bc 100644 --- a/NEWS.md +++ b/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 diff --git a/README.md b/README.md index 75654e2..664774d 100644 --- a/README.md +++ b/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 -``` -