v 0.5

Dockerfile

@@ -2,7 +2,7 @@
 #Dockerfile_ready
 #::::::::::::::
 # The following image is based on shiny-verse, i.e. provides a shiny server
-FROM eugloh/analycyte_base:0.4
+FROM eugloh/analycyte_base:0.5
 
 USER root
 

Dockerfile_base

 #::::::::::::::
 #Dockerfile_base
 #::::::::::::::
-FROM rocker/shiny-verse
+FROM rocker/shiny-verse:latest
 
 # Add quarto binaries
 RUN /rocker_scripts/install_quarto.sh 1.3.450 
@@ -12,10 +12,18 @@ USER root
 RUN apt-get update -qq; \
   apt-get -y --no-install-recommends install libssl-dev libcurl4-openssl-dev xdg-utils libglpk-dev vim;
 
+
+# Install Git
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    git-core \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+
 # Install packages for analycyte
 # 
 
-RUN R -e 'BiocManager::install(c("ade4", "bsplus", "Cairo","checkmate", "colorRamp2", "ComplexHeatmap", "config", "cowplot", "datamods", "data.table", "diffcyt", "dplyr", "DT", "factoextra", "flowCore", "forcats", "fs", "ggiraph", "ggplot2", "ggpubr", "ggrepel", "golem", "grDevices", "grid", "here", "htmlwidgets", "kableExtra", "knitr", "lubridate", "magrittr", "methods", "openxlsx", "patchwork", "plotly", "purrr", "pander","quarto", "randomcoloR", "RColorBrewer", "reactable", "readr", "rlang", "rmarkdown", "rstudioapi", "sessioninfo", "shiny", "shinydashboard", "shinyFiles", "shinyjs", "shinyWidgets", "SingleCellExperiment", "stats", "stringr", "SummarizedExperiment", "shinycssloaders", "testthat", "tibble", "tibble", "tidyr", "utils", "vctrs", "withr", "zip","ggprism"), ask = FALSE, update = FALSE)' 
+RUN R -e 'BiocManager::install(c("ade4", "bsplus", "Cairo","checkmate", "colorRamp2", "ComplexHeatmap", "config", "cowplot", "datamods", "data.table", "diffcyt", "dplyr", "DT", "esquisse","factoextra", "flowCore", "forcats", "fs", "ggiraph", "ggplot2", "ggpubr", "ggrepel", "golem", "grDevices", "grid", "here", "htmlwidgets", "kableExtra", "knitr", "lubridate", "magrittr", "methods", "openxlsx", "patchwork", "plotly", "purrr", "pander","quarto", "randomcoloR", "RColorBrewer", "reactable", "readr", "remotes", "rlang", "rmarkdown", "rstudioapi", "sessioninfo", "shiny", "shinydashboard", "shinyFiles", "shinyjs", "shinyWidgets", "SingleCellExperiment", "stats", "stringr", "SummarizedExperiment", "shinycssloaders", "testthat", "tibble", "tibble", "tidyr", "utils", "vctrs", "withr", "zip","ggprism"), ask = FALSE, update = FALSE)' 
 
 
 # "MatrixGenerics", "S4Vectors",  # implicit installation

README.md

@@ -28,7 +28,7 @@ To develop and test new features in the application, use a Linux host with Docke
 Start analycyte with the base image and a port for shiny web service. The base image is run in interactive mode, otherwise a shiny server is executed (see the FROM item). The base image is pulled from DockerHub on the first run because it does not exist in the local host cache.
 
 ```
-docker run -it -p 3838:3838 eugloh/analycyte_base:0.4 bash
+docker run -it -p 3838:3838 eugloh/analycyte_base:0.5 bash
 ```
 
 Then install the latest version of the analycyte packages.
@@ -94,14 +94,14 @@ docker build -f Dockerfile_base -t analycyte_base .
 Tag the build.
 
 ```
-docker tag analycyte_base eugloh/analycyte_base:0.4
+docker tag analycyte_base eugloh/analycyte_base:0.5
 ```
 
 Login dockerhub, then push the image (you must have an account on DockerHub).
 
 ```
 docker login
-docker push eugloh/analycyte_base:0.4
+docker push eugloh/analycyte_base:0.5
 ```
 
 ## Helping knowledge