update or tweak pkg to run shiny application via Docker

DESCRIPTION

@@ -41,7 +41,8 @@ Imports:
     factoextra,
     reactable,
     dnet,
-    hypeR
+    hypeR,
+    markdown
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.1.1

Dockerfile.shiny

@@ -0,0 +1,50 @@
+# Build according to a specified version of R
+ARG R_VERSION
+ARG R_VERSION=${R_VERSION:-4.1.0}
+
+############# Build Stage: base ##################
+
+# Get shiny+tidyverse+devtools packages from rocker image
+FROM rocker/shiny-verse:${R_VERSION} as base
+
+# Install system libraries of general use
+RUN apt-get update --allow-releaseinfo-change --fix-missing \
+  && apt-get install -y --no-install-recommends \
+  apt-utils \
+  libglpk-dev \
+  libcurl4-openssl-dev \
+  libxml2-dev \
+  libssl-dev \
+  libxtst6 \
+  libxt6 \
+  xdg-utils \
+  && apt clean autoclean \
+  && apt autoremove --yes \
+  && rm -rf /var/lib/{apt,dpkg,cache,log}/
+
+# Create package directory 
+ENV PACKAGE_DIR=/bieulergy  
+
+# Make package as working directory
+WORKDIR ${PACKAGE_DIR}
+
+# Copy package code to Docker image
+COPY . ${PACKAGE_DIR}
+
+# Install all package dependencies
+RUN Rscript "${PACKAGE_DIR}/install_r_packages.R"
+
+# Install package
+RUN Rscript -e 'pkg_dir <- Sys.getenv("PACKAGE_DIR"); devtools::install(pkg_dir, dependencies=TRUE)'
+
+# Copy bash script that starts shiny-server 
+COPY inst/shiny/shiny-server.sh /user/bin/shiny-server.sh
+
+# Allow permissions to execute the bash script
+RUN chmod a+x /user/bin/shiny-server.sh
+
+# Make Shiny app available at port 3838
+EXPOSE 3838
+
+# Execute the bash script to launch shiny app 
+CMD ["/bin/bash", "-c", "/user/bin/shiny-server.sh"]

R/app.R

@@ -6,8 +6,8 @@
 #' @importFrom shiny runApp
 #'
 #' @export
-run.shiny <- function(launch.browser=TRUE, dev=TRUE) {
+run.shiny <- function(launch.browser=TRUE, dev=TRUE, host='0.0.0.0', port=3838) {
     app.dir <- system.file("shiny", package="bieulergy")
     if (dev) options(shiny.autoreload=TRUE)
-    shiny::runApp(app.dir, launch.browser=launch.browser, display.mode="normal")
+    shiny::runApp(app.dir, launch.browser=launch.browser, display.mode="normal", host=host, port=port)
 }

docker-compose.yml

@@ -0,0 +1,22 @@
+version: '3.9'
+
+x-r-version:
+  &r-version
+  R_VERSION=4.1.0
+
+x-bieulergy-git-repo:
+  &bieulergy-git-repo
+  https://github.com/montilab/bieulergy.git#dev
+
+services:
+  bieulergy:
+    container_name: bieulergy
+    image: montilab/bieulergy:latest
+    build: 
+      context: *bieulergy-git-repo
+      dockerfile: Dockerfile.shiny
+      args:
+        - *r-version
+    restart: always
+    ports:
+      - 1234:3838

inst/shiny/run_bieulergy_shiny.R

@@ -0,0 +1,10 @@
+
+# Load R packages
+library(shiny)
+library(bieulergy)
+
+# Set limitation for uploading files
+options(shiny.maxRequestSize=30*1024^2)
+
+# Create a shiny app object
+bieulergy::run.shiny(host='0.0.0.0', port=3838)

inst/shiny/shiny-server.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+PACKAGE_DIR=/bieulergy
+
+# Make sure the directory for individual app logs exists
+mkdir -p /var/log/shiny-server
+chown shiny.shiny /var/log/shiny-server
+
+if [ "$APPLICATION_LOGS_TO_STDOUT" != "false" ];
+then
+# push the "real" application logs to stdout with xtail in detached mode
+exec xtail /var/log/shiny-server/ &
+  fi
+
+# Start shiny server
+exec Rscript $PACKAGE_DIR/inst/shiny/run_bieulergy_shiny.R 2>&1

install_r_packages.R

@@ -0,0 +1,49 @@
+
+# Create a list of start-up packages 
+startup_packages <- c("BiocManager", "dplyr", "rvest", "xml2", "yaml")
+
+# Select only the packages that aren't currently installed in the system
+install_startup_packages <- startup_packages[which(!startup_packages %in% utils::installed.packages())]
+
+# And finally we install the required packages
+for(pkg in install_startup_packages) utils::install.packages(pkg, dependencies=TRUE, repos='http://cran.rstudio.com/')
+
+# Load packages
+library(BiocManager)
+library(dplyr)
+library(rvest)
+library(xml2)
+library(yaml)
+
+# Get all available Bioconductor packages
+url <- 'https://www.bioconductor.org/packages/release/bioc/'
+biocPackages <- url %>% 
+  xml2::read_html() %>% 
+  rvest::html_table() %>%
+  .[[1]] %>%
+  dplyr::select(Package) %>% 
+  dplyr::mutate(source = 'BioConductor')
+
+# Read in package dependencies in DESCRIPTION
+DESCRIPTION <- yaml::read_yaml("DESCRIPTION")
+
+# Extract all imports packages
+required_pkgs <- trimws(strsplit(DESCRIPTION$Imports, ",", fixed=TRUE)[[1]])
+
+# Extract all required Bioconductor packages
+bioconductor_pkgs <- required_pkgs[which(required_pkgs %in% biocPackages$Package)]
+
+# Select only the packages that aren't currently installed in the system
+install_bioconductor_pkgs <- bioconductor_pkgs[which(!bioconductor_pkgs %in% utils::installed.packages())]
+
+# And finally we install the required packages
+for(pkg in install_bioconductor_pkgs) BiocManager::install(pkg)
+
+# Extract all required CRAN packages
+cran_pkgs <- required_pkgs[which(!required_pkgs %in% bioconductor_pkgs)]
+
+# Select only the packages that aren't currently installed in the system
+install_cran_pkgs <- cran_pkgs[which(!cran_pkgs %in% utils::installed.packages())]
+
+# And finally we install the required packages including their dependencies
+for(pkg in install_cran_pkgs) utils::install.packages(pkg, dependencies=TRUE, repos='http://cran.rstudio.com/')