Add conda installation and improve library loading

LoadPackages.R

@@ -4,23 +4,21 @@ options(bitmapType='cairo')
 if (!require("Rcpp")){
   install.packages("Rcpp",  repos="https://cran.univ-paris1.fr/")
 }
+
 if(!require(shiny)){
   install.packages("shiny",  repos="https://cran.univ-paris1.fr/")
-  library(shiny)
 }
 
 if(!require(rjson)){
   install.packages('rjson',  repos="https://cran.univ-paris1.fr/")
-  library(rjson)
 }
+
 if(!require(ape)){
   install.packages('ape',  repos="https://cran.univ-paris1.fr/")
-  library(ape)
 }
 
 if(!require(GUniFrac)){
   install.packages('GUniFrac',  repos="https://cran.univ-paris1.fr/")
-  library(GUniFrac)
 }
 
 if (!require(psych)) {
@@ -30,25 +28,20 @@ if (!require(psych)) {
 
 if (!require(ggplot2)) {
   install.packages('ggplot2',  repos="https://cran.univ-paris1.fr/")
-  library(ggplot2)
 }
 
 if (!require(vegan)) {
   install.packages('vegan',  repos="https://cran.univ-paris1.fr/")
-  library(vegan)
 }
 
 if (!require(dendextend)) {
   install.packages('dendextend',  repos="https://cran.univ-paris1.fr/")
-  library(dendextend)
 }
 
 if (!require(circlize)) {
   install.packages('circlize',  repos="https://cran.univ-paris1.fr/")
-  library(circlize)
 }
 
-
 # if (!require(BiocInstaller)){
 #   source("https://bioconductor.org/biocLite.R")
 #   biocLite("BiocInstaller")
@@ -60,214 +53,169 @@ if(!require(BiocManager)){
 }
 if (!require(genefilter)) {
   BiocManager::install("genefilter", ask=FALSE)
-  library(genefilter)
 }
 
 if(!require("SummarizedExperiment")){
   BiocManager::install("SummarizedExperiment", ask=FALSE)
-  library(SummarizedExperiment)
 }
 
 if (!require(googleVis)) {
   install.packages('googleVis',  repos="https://cran.univ-paris1.fr/")
-  suppressPackageStartupMessages(library(googleVis))
+  #suppressPackageStartupMessages(library(googleVis))
 }
 
 if (!require(shinyjs)) {
   install.packages('shinyjs',  repos="https://cran.univ-paris1.fr/")
-  library(shinyjs)
 }
 
 if (!require(DT)) {
   install.packages('DT',  repos="https://cran.univ-paris1.fr/")
-  library(DT)
 }
 
 if (!require(RColorBrewer)) {
   install.packages('RColorBrewer',  repos="https://cran.univ-paris1.fr/")
-  library(RColorBrewer)
 }
 
 if (!require(gplots)) {
   install.packages('gplots',  repos="https://cran.univ-paris1.fr/")
-  library(gplots)
 }
 
 if (!require(ade4)) {
   install.packages('ade4',  repos="https://cran.univ-paris1.fr/")
-  library(ade4)
 }
 
 if (!require(scales)) {
   install.packages('scales',  repos="https://cran.univ-paris1.fr/")
-  library(scales)
 }
 
 if (!require(phytools)) {
   install.packages('phytools',  repos="https://cran.univ-paris1.fr/")
-  library(phytools)
 }
 
 if(!require(philentropy)){
   install.packages("philentropy",  repos="https://cran.univ-paris1.fr/")
-  library(philentropy)
 }
 
 if (!require("shinyWidgets")){
   install.packages("shinyWidgets")
   #devtools::install_github("aghozlane/shinyWidgets")
-  library(shinyWidgets)
 }
 
 if (!require("sendmailR")){
   install.packages("sendmailR",  repos="https://cran.univ-paris1.fr/")
-  library(sendmailR)
 }
 
 if (!require("shinyBS")){
   install.packages("shinyBS",  repos="https://cran.univ-paris1.fr/")
-  library(shinyBS)
 }
 
 library(tools)
 
 if (!require("flexdashboard")){
   install.packages("flexdashboard",  repos="https://cran.univ-paris1.fr/")
-  library(flexdashboard)
 }
 
 if (!require("backports")){
   install.packages("backports",  repos="https://cran.univ-paris1.fr/")
-  library(backports)
 }
 
 
 if (!require("readr")){
   install.packages("readr",  repos="https://cran.univ-paris1.fr/")
-  library(readr)
 }
 
 if (!require("jsonlite")){
   install.packages("jsonlite",  repos="https://cran.univ-paris1.fr/")
-  library(jsonlite)
 }
 
-
 if (!require("shinyFiles")){
   install.packages("shinyFiles",  repos="https://cran.univ-paris1.fr/")
-  library(shinyFiles)
 }
 
 if (!require("htmltools")){
   install.packages("htmltools",  repos="https://cran.univ-paris1.fr/")
-  library(htmltools)
 }
 
-# if (!require("V8")){
-#   install.packages("V8",  repos="https://cran.univ-paris1.fr/")
-#   library(htmltools)
-# }
-
-# if(!require(plotly)){
-#   install.packages("plotly")
-#   library(plotly)  
-# }
-
 if (!require("rAmCharts")){
   install.packages("rAmCharts",  repos="https://cran.univ-paris1.fr/")
-  library(rAmCharts)
 }
 
 if(!require("colourpicker")){
   install.packages("colourpicker",  repos="https://cran.univ-paris1.fr/")
-  library(colourpicker)
 }
 
 if(!require("data.table")){
   install.packages("data.table",  repos="https://cran.univ-paris1.fr/")
-  library(data.table)
 }
 
 if(!require("UpSetR")){
   install.packages("UpSetR",  repos="https://cran.univ-paris1.fr/")
-  library(UpSetR)
 }
 
 if(!require("ggrepel")){
   install.packages("ggrepel",  repos="https://cran.univ-paris1.fr/")
-  library(ggrepel)
 }
 
-# if(!require("networkD3")){
-#   install.packages("networkD3")
-#   library(networkD3)
-# }
-
 if(!require("igraph")){
   install.packages("igraph",  repos="https://cran.univ-paris1.fr/")
-  library(igraph)
 }
 
 if(!require("visNetwork")){
   install.packages("visNetwork",  repos="https://cran.univ-paris1.fr/")
-  library(visNetwork)
 }
 
 if (!require("shinytoastr")){
-  install.packages("shinytoastr")
-  library(shinytoastr)
+  install.packages("shinytoastr",  repos="https://cran.univ-paris1.fr/")
 }
 
 if (!require("scatterD3")) {
   #devtools::install_github('aghozlane/scatterD3')
   install.packages("scatterD3", repos="https://cran.univ-paris1.fr/")
-  library(scatterD3)
 }
 
 if (!require(devtools)) {
   install.packages('devtools',  repos="https://cran.univ-paris1.fr/")
-  library(devtools)
 }
 
 if(!require("shinydashboardshaman")){
   devtools::install_github('aghozlane/shinydashboardshaman')
-  library(shinydashboardshaman)
 }
 
 if (!require("d3heatmap")) {
   #devtools::install_github('aghozlane/d3heatmap')
   devtools::install_github("rstudio/d3heatmap")
-  library(d3heatmap)
 }
 
-# Let us use biomformat instead of biom
-#torename
 if (!require("biomformatshaman")){
   devtools::install_github("aghozlane/biomformatshaman")
-  library(biomformatshaman)
 }
 
 if (!require("rNVD3shaman")) {
   devtools::install_github('aghozlane/rNVD3shaman')
-  library(rNVD3shaman)
 }
 
 if (!require("DESeq2shaman")) {
   devtools::install_github("aghozlane/DESeq2shaman")
-  library(DESeq2shaman)
 }
 
 if(!require("PhyloTreeMetaR")){
   devtools::install_github("pierreLec/PhyloTreeMetaR")
-  library(PhyloTreeMetaR)
 }
 
 if(!require("treeWeightD3")){
   devtools::install_github('pierreLec/treeWeightD3')
-  library(treeWeightD3)
 }
 
 if(!require("d3vennR")){
   devtools::install_github("timelyportfolio/d3vennR")
-  library(d3vennR)
-}
\ No newline at end of file
+}
+
+libshaman=c("shiny", "rjson", "ape", "GUniFrac", "psych", "ggplot2", "vegan", "dendextend", 
+            "circlize", "genefilter", "SummarizedExperiment", "shinyjs", "DT", "RColorBrewer", 
+            "gplots", "ade4", "scales", "phytools", "philentropy", "shinyWidgets", "sendmailR", 
+            "shinyBS", "tools", "flexdashboard", "backports", "readr", "jsonlite", "shinyFiles", 
+            "htmltools", "rAmCharts", "colourpicker", "data.table", "UpSetR", "ggrepel", "igraph", 
+            "visNetwork", "shinytoastr", "scatterD3", "devtools", "shinydashboardshaman", "d3heatmap", 
+            "biomformatshaman", "rNVD3shaman", "DESeq2shaman", "PhyloTreeMetaR", "treeWeightD3", "d3vennR",
+            "googleVis")
+lapply(libshaman, require, character.only = TRUE)
\ No newline at end of file

ui.R

@@ -241,16 +241,20 @@ function(request) {
                                                            br(),"shiny::runGitHub('aghozlane/shaman')"),width=9,class="mainwell")),
                                     
                                     tabPanel("R install",
-                                             p("SHAMAN is available for R=3.6.1. A more recent installation of R will break the differential abundance interface. The installation, download and execution can all be performed with a small R script:",style = "font-family: 'times'; font-si16pt"),
+                                             p("SHAMAN is available for R=3.6.1. Of note, raw data submission is not possible with this version. The installation, download and execution can all be performed with a small R script:",style = "font-family: 'times'; font-si16pt"),
                                              mainPanel(div(style = 'max-width: 900px; word-wrap: break-word;',"# Load shiny packages",br(),
                                                            "if(!require('shiny')){",br(),"  install.packages('shiny')",br(),"}",br(),
                                                            "system(\"Rscript -e 'shiny::runGitHub(\\\"pierreLec/KronaRShy\\\",port=5438)'\",wait=FALSE)",
                                                            br(),"# Install dependencies,",br(),"# download last version from github,",br(),"# and run SHAMAN in one command:",br(),
                                                            "shiny::runGitHub('aghozlane/shaman')"),width=9,class="mainwell"),
-                                             p("This script can also be dowloaded", a("here", target="_blank", href="shamanapp.R"), "and executed as following :"),
-                                             mainPanel(div(style = 'max-width: 900px; word-wrap: break-word;',"chmod +x ./shamanapp.R && Rscript ./shamanapp.R"),width=6,class="mainwell"),br(),
-                                             p("Of note, contribution to SHAMAN code are always welcome and can be performed with the", a("github deposit.",href="https://github.com/aghozlane/shaman")))
-                                    
+                                             p("This script can also be dowloaded", a("here", target="_blank", href="shaman.R"), "and executed as following :"),
+                                             mainPanel(div(style = 'max-width: 900px; word-wrap: break-word;',"chmod +x ./shaman.R && Rscript ./shaman.R"),width=6,class="mainwell"),br(),
+                                             p("Of note, contribution to SHAMAN code are always welcome and can be performed with the", a("github deposit.",href="https://github.com/aghozlane/shaman"))),
+                                    tabPanel("Conda install",
+                                             p("Conda installation of SHAMAN can be performed as follow: ",style = "font-family: 'times'; font-si16pt"),
+                                             mainPanel(div(style = 'max-width: 900px; word-wrap: break-word;',
+                                                           "# Download and install SHAMAN", br(),"conda install -c aghozlane shaman", br(),
+                                                           "# Now run shaman", br(), "shaman"), width=6,class="mainwell"))
                              )
                          )
                   )

www/shaman_conda.R

+#!/usr/bin/Rscript --vanilla
+system("Rscript -e 'library(\"shiny\");runApp(appDir= KronaRShy\", port=5438)'",wait=FALSE)
+runGitHub("aghozlane/shaman")