Proto

.gitignore

@@ -31,3 +31,4 @@ vignettes/*.pdf
 # Temporary files created by R markdown
 *.utf8.md
 *.knit.md
+.Rproj.user

R/menugauche.R

+MenuGauche = sidebarMenu(id = "sidebarmenu",
+                         menuItem("Home", tabName = "Home",  icon = icon("home", lib="font-awesome")),
+                         
+                         tags$br(), tags$br(), tags$br(),
+                         
+                         menuItem("Team", icon = icon("book", lib="font-awesome"),
+                                  menuItem("Jimmy Lopez",  href = "http://www.isem.univ-montp2.fr/recherche/les-plate-formes/bioinformatique-labex/personnel/", newtab = TRUE,   icon = shiny::icon("male"), selected = NULL  )
+                         )
+                         
+)

RPACIB.Rproj

+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX

app.R

+library(shiny)
+library(shinydashboard)
+library(shinyjs)
+library(shinycssloaders)
+library(DT)
+library(dplyr)
+
+source("./R/menugauche.R", local = T)
+source("./pages/pages_def_home.R", local = T)
+
+options(encoding = 'UTF-8')
+
+#style <- tags$style(HTML(readLines("www/added_styles.css")) )
+UI <- dashboardPage(
+  skin = "green",
+  dashboardHeader(title = "RPACIB"),
+  dashboardSidebar(MenuGauche),
+  dashboardBody(
+    
+    shinyjs::useShinyjs(),
+    tags$head(tags$link(rel = "stylesheet", type = "text/css", href = "bootstrap.min.readable.css")) ,
+    #tags$head(style),
+
+    tabItems(
+      tabItem(tabName = "Home",         tabHome)
+    )
+  )
+)
+
+
+
+server <- function( input, output, session) {
+  
+  shinyCheckBoxPackage <- function(df ) {
+    inputs = sprintf('<input id="%s" type="checkbox">', df[,"Package"])
+    inputs
+  }
+  
+  allCRAN <<- as.data.frame(available.packages()[, c("Package", "Version")])
+  allBIO <<- as.data.frame(available.packages(repo = biocinstallRepos()[1])[, c("Package", "Version")])
+  
+  hide("downloadContainerFile")
+  
+  #allCRAN$select <- sprintf('<input id="chekcboxCRAN_%s" type="checkbox" onclick=\"Shiny.onInputChange(&#39;select_cran_package&#39;,  this.id)\">', allCRAN[,"Package"])
+  #allBIO$select <- sprintf('<input id="chekcboxBIO_%s" type="checkbox">', allBIO[,"Package"])
+  
+  #allCRAN <- allCRAN[c("select", "Package", "Version")]
+  #allBIO <- allBIO[c("select", "Package", "Version")]
+  
+  source("./server/opt_home.R", local=TRUE)
+}
+
+shinyApp(ui = UI, server = server)
\ No newline at end of file

pages/pages_def_home.R

+tabHome = fluidPage(align="left",
+  
+                    column(width = 2,
+                           box(
+                               title = "Params",
+                               width = NULL,
+                               collapsible = TRUE,
+                               solidHeader = TRUE,
+                               status="primary",
+                               
+                               textInput("imageName", "Image Name", ""),
+                               br(),
+                               radioButtons("containerType", "Container type:", choices = list("Singularity" = "singularity"), selected = "singularity"),
+                               br(),
+                               textAreaInput("customDataContainer", "Add custom line to container file:"),
+                               br(), br(),
+                               actionButton("createContainer", label = "Create", icon("paper-plane"), style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
+                               downloadButton('downloadContainerFile', label = "Dowload",  style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
+                               
+
+                            
+                               
+                               
+                           )),
+                    column(width = 10,
+                           box(
+                             title = "R Packages",
+                             width = NULL,
+                             collapsible = TRUE,
+                             solidHeader = TRUE,
+                             status="primary",
+                             tabsetPanel( id='rpackages',
+                                          tabPanel('CRAN',    
+                                            withSpinner(DT::dataTableOutput('dtrcranpackage'), type = 4, proxy.height = "150px")
+                                          ),
+                                          tabPanel('Bioconductor',   
+                                            DT::dataTableOutput('dtrbioconductorpackage')),
+                                          tabPanel('Github',
+                                            DT::dataTableOutput('dtrgithubpackage'))
+                             )
+                          )
+                    ),
+                    column(width = 12,
+                           box(
+                             title = "Preview File:",
+                             width = NULL,
+                             collapsible = TRUE,
+                             solidHeader = TRUE,
+                             status="primary",
+                             style='height:1000px; overflow-y: scroll',
+                             verbatimTextOutput("previewContainer")
+                           )
+                    )
+                    
+)
\ No newline at end of file

server/opt_home.R

+
+output$dtrcranpackage <- DT::renderDataTable({
+  
+  
+  result <- allCRAN
+  
+  return(result)
+}, filter='top', escape = FALSE, rownames= FALSE,server = TRUE)
+
+output$dtrbioconductorpackage <- DT::renderDataTable({
+  result <- allBIO
+  
+  return(result)
+}, filter='top', escape = FALSE, rownames= FALSE,server = TRUE)
+
+output$dtrgithubpackage <- DT::renderDataTable({
+  result <- data.frame(Package=character(),
+                             Version=character())
+  
+  return(result)
+}, filter='top', escape = FALSE, rownames= FALSE,server = TRUE)
+
+
+createContentFile <- function() {
+  result <- "Bootstrap: docker"
+  result <- paste(result, "From: ubuntu:16.04", sep = "\n")
+  result <- paste(result, "IncludeCmd: yes", sep = "\n")
+  
+  result <- paste(result, "\n", sep = "\n")
+  
+  result <- paste(result, "%environment", sep = "\n")
+  result <- paste(result, "\tR_VERSION=3.4.3", sep = "\n")
+  result <- paste(result, "\texport R_VERSION", sep = "\n")
+  result <- paste(result, "\tR_CONFIG_DIR=/etc/R/", sep = "\n")
+  result <- paste(result, "\texport R_CONFIG_DIR", sep = "\n")
+  
+  result <- paste(result, "\n", sep = "\n")
+  
+  result <- paste(result, "%labels", sep = "\n")
+  result <- paste(result, "\tAuthor Jimmy Lopez", sep = "\n")
+  result <- paste(result, "\tVersion v0.0.1", sep = "\n")
+  result <- paste(result, "\tR_Version 3.4.3", sep = "\n")
+  result <- paste0(result, "\n\tbuild_date ", format(Sys.time(), "%Y %b %d"), "\n")
+  
+  result <- paste(result, "\n", sep = "\n")
+  
+  result <- paste(result, "%apprun R", sep = "\n")
+  result <- paste(result, '\texec R "$@"', sep = "\n")
+  
+  result <- paste(result, "\n", sep = "\n")
+  
+  result <- paste(result, "%apprun Rscript", sep = "\n")
+  result <- paste(result, '\texec Rscript "$@"', sep = "\n")
+  
+  result <- paste(result, "\n", sep = "\n")
+  
+  result <- paste(result, "%runscript", sep = "\n")
+  result <- paste(result, '\texec R "$@"', sep = "\n")
+  
+  result <- paste(result, "%post", sep = "\n")
+  result <- paste(result, "\tapt-get update", sep = "\n")
+  result <- paste(result, "\tapt-get install -y wget libblas3 libblas-dev liblapack-dev liblapack3 curl", sep = "\n")
+  result <- paste(result, "\tapt-get install -y gcc fort77 aptitude", sep = "\n")
+  result <- paste(result, "\taptitude install -y g++ xorg-dev libreadline-dev  gfortran", sep = "\n")
+  result <- paste(result, "\tapt-get install -y libssl-dev libxml2-dev libpcre3-dev liblzma-dev libbz2-dev libcurl4-openssl-dev", sep = "\n")
+  result <- paste(result, "\tapt-get update", sep = "\n")
+  
+  result <- paste(result, "\n", sep = "\n")
+  
+  result <- paste(result, '\tcd $HOME', sep = "\n")
+  result <- paste(result, '\twget https://cran.rstudio.com/src/base/R-3/R-3.4.3.tar.gz', sep = "\n")
+  result <- paste(result, '\ttar xvf R-3.4.3.tar.gz', sep = "\n")
+  result <- paste(result, '\tcd R-3.4.3', sep = "\n")
+  result <- paste(result, "\t./configure --enable-R-static-lib --with-blas --with-lapack --enable-R-shlib=yes ", sep = "\n") 
+  result <- paste(result, "\tmake", sep = "\n") 
+  result <- paste(result, "\tmake install", sep = "\n") 
+  
+  result <- paste(result, "\n", sep = "\n")
+  
+  selectCRAN <- allCRAN[input$dtrcranpackage_rows_selected,]
+  selectCRAN <- selectCRAN[,"Package"]
+  sizeCRAN <- length(selectCRAN)
+  listRCRAN <- '\techo install.packages\\(c('
+  for (pkg in 1:sizeCRAN){
+    if(pkg < sizeCRAN) {
+      listRCRAN <- paste0(listRCRAN, '"',selectCRAN[pkg],'", ')
+    } else {
+      listRCRAN <- paste0(listRCRAN, '"',selectCRAN[pkg],'"), repos\\=\'https://cloud.r-project.org\'\\) | R --slave ')
+    }
+  }
+  result <- paste(result, listRCRAN, sep = "\n")
+  
+  result <- paste(result, "\n", sep = "\n")
+  
+  result <- paste(result, '\tR --slave -e "source(\'https://bioconductor.org/biocLite.R\'); \\', sep = "\n")
+  result <- paste(result, "\tbiocLite()\n", sep = "\n")
+  
+  selectBIO <- allBIO[input$dtrbioconductorpackage_rows_selected,]
+  selectBIO <- selectBIO[,"Package"]
+  sizeBIO <- length(selectBIO)
+  listRBIO <- '\tR --slave -e "source(\'https://bioconductor.org/biocLite.R\'); \\'
+  listRBIO <- paste0(listRBIO, "\n\tbiocLite(")
+  for (pkg in 1:sizeBIO){
+    if(pkg < sizeBIO) {
+      listRBIO <- paste0(listRBIO, '"',selectCRAN[pkg],'", ')
+    } else {
+      listRBIO <- paste0(listRBIO, '"',selectCRAN[pkg],'")')
+    }
+  }
+  result <- paste(result, listRBIO, sep = "\n")
+  
+  result <- paste(result, "\n", sep = "\n")
+  result <- paste(result, "\n", sep = "\n")
+  
+  result <- paste(result, input$customDataContainer, sep = "\t\n")
+  return(result)
+}
+
+createContainerPackage <- eventReactive(input$createContainer, {
+
+  result <- createContentFile()
+  
+  show("downloadContainerFile")
+  
+  HTML(result)
+})
+
+
+
+output$previewContainer <- renderText({
+  createContainerPackage()
+})
+
+output$downloadContainerFile <- downloadHandler(
+  filename = function() {
+    paste("Singularity",input$imageName, sep = ".")
+  },
+  content = function(file) {
+    print(file)
+    result <- createContentFile()
+    print(result)
+    write(result,file=file)
+  }
+)
+
+