Commit a1a9c8cd authored by Amine  GHOZLANE's avatar Amine GHOZLANE
Browse files

Add conda installation and improve library loading

parent 5d520be3
Pipeline #13936 passed with stage
in 46 minutes and 49 seconds
......@@ -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
......@@ -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"))
)
)
)
......
#!/usr/bin/Rscript --vanilla
system("Rscript -e 'library(\"shiny\");runApp(appDir= KronaRShy\", port=5438)'",wait=FALSE)
runGitHub("aghozlane/shaman")
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