diff --git a/README.md b/README.md index 5e0e9a6..2eca67d 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,3 @@ - # scdrake [![NEWS: @@ -114,27 +113,21 @@ you can use `singularity pull docker-daemon:` You can pull the Docker image with the latest stable `{scdrake}` version using -``` bash -docker pull jirinovo/scdrake:1.5.2 -singularity pull docker:jirinovo/scdrake:1.5.2 -``` + docker pull jirinovo/scdrake:1.6.0 + singularity pull docker:jirinovo/scdrake:1.6.0 or list available versions in [our Docker Hub repository](https://hub.docker.com/r/jirinovo/scdrake/tags). For the latest development version use -``` bash -docker pull jirinovo/scdrake:latest -singularity pull docker:jirinovo/scdrake:latest -``` + docker pull jirinovo/scdrake:latest + singularity pull docker:jirinovo/scdrake:latest **Note for Mac users with M1/M2 chipsets**: until version 1.5.0 (inclusive), `arm64` images are available. -``` bash -docker pull jirinovo/scdrake:1.5.0-bioc3.15-arm64 -``` + docker pull jirinovo/scdrake:1.5.0-bioc3.15-arm64 ### Running the container @@ -143,39 +136,33 @@ and Windows or MacOS running Docker Desktop. First make a shared directory that will be mounted to the container: -``` bash -mkdir ~/scdrake_projects -cd ~/scdrake_projects -``` + mkdir ~/scdrake_projects + cd ~/scdrake_projects And run the image that will expose RStudio Server on port 8787 on your host: -``` bash -docker run -d \ - -v $(pwd):/home/rstudio/scdrake_projects \ - -p 8787:8787 \ - -e USERID=$(id -u) \ - -e GROUPID=$(id -g) \ - -e PASSWORD=1234 \ - jirinovo/scdrake:1.5.2 -``` + docker run -d \ + -v $(pwd):/home/rstudio/scdrake_projects \ + -p 8787:8787 \ + -e USERID=$(id -u) \ + -e GROUPID=$(id -g) \ + -e PASSWORD=1234 \ + jirinovo/scdrake:1.6.0 For Singularity, also make shared directories and execute the container (“run and forget”): -``` bash -mkdir -p ~/scdrake_singularity -cd ~/scdrake_singularity -mkdir -p home/${USER} scdrake_projects -singularity exec \ - -e \ - --no-home \ - --bind "home/${USER}/:/home/${USER},scdrake_projects/:/home/${USER}/scdrake_projects" \ - --pwd "/home/${USER}/scdrake_projects" \ - path/to/scdrake_image.sif \ - scdrake -``` + mkdir -p ~/scdrake_singularity + cd ~/scdrake_singularity + mkdir -p home/${USER} scdrake_projects + singularity exec \ + -e \ + --no-home \ + --bind "home/${USER}/:/home/${USER},scdrake_projects/:/home/${USER}/scdrake_projects" \ + --pwd "/home/${USER}/scdrake_projects" \ + path/to/scdrake_image.sif \ + scdrake ## Installing `{scdrake}` manually (not recommended) @@ -191,7 +178,7 @@ Click for details - For MacOS: `$ brew install libxml2 imagemagick@6 harfbuzz fribidi libgit2 geos pandoc` -### Install R \>= 4.2 +### Install R >= 4.2 See @@ -204,34 +191,26 @@ management of local R libraries. It is intended to be used on a per-project basis, i.e. each project should use its own library of R packages. -``` r -install.packages("renv") -``` + install.packages("renv") ### Initialize a new `{renv}` library Switch to directory where you will analyze data and initialize a new `{renv}` library: -``` r -renv::consent(TRUE) -renv::init() -``` + renv::consent(TRUE) + renv::init() Now exit and run again R. You should see a message that renv library has been activated. ### Install BiocManager -``` r -renv::install("BiocManager") -``` + renv::install("BiocManager") ### Install Bioconductor 3.15 -``` r -BiocManager::install(version = "3.15") -``` + BiocManager::install(version = "3.15") ### Restore `{scdrake}` dependencies from lockfile @@ -239,19 +218,15 @@ BiocManager::install(version = "3.15") packages (and other things) into a lockfile. Such lockfile is available for `{scdrake}` and you can use it to install all dependencies by -``` r -## -- This is a lockfile for the latest stable version of scdrake. -download.file("https://raw.githubusercontent.com/bioinfocz/scdrake/1.5.2/renv.lock") -## -- You can increase the number of CPU cores to speed up the installation. -options(Ncpus = 2) -renv::restore(lockfile = "renv.lock", repos = BiocManager::repositories()) -``` + ## -- This is a lockfile for the latest stable version of scdrake. + download.file("https://raw.githubusercontent.com/bioinfocz/scdrake/1.6.0/renv.lock") + ## -- You can increase the number of CPU cores to speed up the installation. + options(Ncpus = 2) + renv::restore(lockfile = "renv.lock", repos = BiocManager::repositories()) For the lockfile for the latest development version use -``` r -download.file("https://raw.githubusercontent.com/bioinfocz/scdrake/main/renv.lock") -``` + download.file("https://raw.githubusercontent.com/bioinfocz/scdrake/main/renv.lock") ### Install the `{scdrake}` package @@ -259,14 +234,12 @@ Now we can finally install the `{scdrake}` package, but using a non-standard approach - without its dependencies (which are already installed from the lockfile). -``` r -remotes::install_github( - "bioinfocz/scdrake@1.5.2", - dependencies = FALSE, upgrade = FALSE, - keep_source = TRUE, build_vignettes = TRUE, - repos = BiocManager::repositories() -) -``` + remotes::install_github( + "bioinfocz/scdrake@1.6.0", + dependencies = FALSE, upgrade = FALSE, + keep_source = TRUE, build_vignettes = TRUE, + repos = BiocManager::repositories() + ) For the latest development version use `"bioinfocz/scdrake"`. @@ -274,9 +247,7 @@ For the latest development version use `"bioinfocz/scdrake"`. Optionally, you can install `{scdrake}`’s CLI scripts with -``` r -scdrake::install_cli() -``` + scdrake::install_cli() CLI should be now accessible as a `scdrake` command. By default, the CLI is installed into `~/.local/bin`, which is usually present in the `PATH` @@ -328,7 +299,7 @@ vignette](https://bioinfocz.github.io/scdrake/articles/scdrake.html) ## Vignettes and other readings See for a documentation website of -the latest stable version (1.5.2) where links to vignettes below become +the latest stable version (1.6.0) where links to vignettes below become real :-) See for a documentation @@ -353,25 +324,25 @@ website of the current development version. - Config files (internals): `vignette("scdrake_config")` - Environment variables: `vignette("scdrake_envvars")` - General configs: - - Pipeline config -\> `vignette("config_pipeline")` - - Main config -\> `vignette("config_main")` + - Pipeline config -> `vignette("config_pipeline")` + - Main config -> `vignette("config_main")` - Pipelines and stages: - Single-sample pipeline: - Stage `01_input_qc`: reading in data, filtering, quality - control -\> `vignette("stage_input_qc")` + control -> `vignette("stage_input_qc")` - Stage `02_norm_clustering`: normalization, HVG selection, SVG selection, dimensionality reduction, clustering, - (manual) cell type annotation -\> + (manual) cell type annotation -> `vignette("stage_norm_clustering")` - Integration pipeline: - - Stage `01_integration`: reading in data and integration -\> - `vignette("stage_integration")` + - Stage `01_integration`: reading in data and integration + -> `vignette("stage_integration")` - Stage `02_int_clustering`: post-integration clustering and - cell annotation -\> `vignette("stage_int_clustering")` + cell annotation -> `vignette("stage_int_clustering")` - Common stages: - - Stage `cluster_markers` -\> + - Stage `cluster_markers` -> `vignette("stage_cluster_markers")` - - Stage `contrasts` (differential expression) -\> + - Stage `contrasts` (differential expression) -> `vignette("stage_contrasts")` We encourage all users to read @@ -393,9 +364,7 @@ Below is the citation output from using `citation("scdrake")` in R. Please run this yourself to check for any updates on how to cite **scdrake**. -``` r -print(citation("scdrake"), bibtex = TRUE) -``` + print(citation("scdrake"), bibtex = TRUE) To cite package ‘scdrake’ in publications use: @@ -431,7 +400,7 @@ but if you need e.g. a general help. If you want to contribute to `{scdrake}`, read the [contribution guide](.github/CONTRIBUTING.md), please. All pull requests are welcome! -:slightly_smiling_face: +:slightly\_smiling\_face: ## Code of Conduct