Move to shinydashboardshaman and prepare autodevops

Dockerfile

+FROM ubuntu:18.04
+
+MAINTAINER Amine Ghozlane "amine.ghozlane@pasteur.fr"
+
+RUN apt-get update && apt-get install -y \
+    wget \
+    gdebi-core \
+    libcurl4-openssl-dev\
+    libcairo2-dev \
+    libjpeg-dev \
+    libtiff5-dev \
+    libxt-dev \
+    libxml2-dev \
+    libxml2 \
+    libreadline6-dev \
+    git \
+    libssl-dev \
+    libssh2-1-dev \
+    libnlopt-dev \
+    python3-pip \
+    python3-yaml \
+    gcc \ 
+    gfortran \ 
+    g++ \
+    make \
+    openjdk-8-jdk \
+    libmagick++-dev 
+    
+RUN pip3 install bioblend python-daemon
+
+#Download and install shiny server
+RUN wget --no-verbose https://cran.r-project.org/src/base/R-3/R-3.6.1.tar.gz -P /opt/ && \
+    tar -zxf /opt/R-3.6.1.tar.gz -C /opt && rm /opt/R-3.6.1.tar.gz && \
+    cd /opt/R-3.6.1/ && ./configure --with-x=no && \
+    make -j 4  && make install && cd / && rm -rf  /opt/R-3.6.1 && \  
+    wget --no-verbose https://s3.amazonaws.com/rstudio-shiny-server-os-build/ubuntu-12.04/x86_64/VERSION -O "version.txt" && \
+    VERSION=$(cat version.txt)  && \
+    wget --no-verbose "https://s3.amazonaws.com/rstudio-shiny-server-os-build/ubuntu-12.04/x86_64/shiny-server-$VERSION-amd64.deb" -O ss-latest.deb && \
+    gdebi -n ss-latest.deb && \
+    rm -f version.txt ss-latest.deb && \
+    wget ftp://shiny01.hosting.pasteur.fr/pub/shaman_package_201908.tar.gz -P /opt && \
+    mkdir /opt/packman
+
+RUN R -e """install.packages('packrat', repos='http://cran.univ-paris1.fr/');library("packrat");packrat::unbundle('/opt/shaman_package_201908.tar.gz', '/opt/packman')"""
+
+COPY docker_inst/shiny-server.conf  /etc/shiny-server/shiny-server.conf
+COPY docker_inst/.Rprofile  /srv/shiny-server/
+
+RUN git clone https://github.com/pworinger/shaman.git /srv/shiny-server/shaman && \
+    #git clone https://github.com/aghozlane/shaman.git /srv/shiny-server/shaman && \
+    git clone https://github.com/pierreLec/KronaRShy.git /srv/shiny-server/kronarshy && \
+    git clone https://github.com/aghozlane/shaman_bioblend.git /usr/bin/shaman_bioblend && \
+    mv /srv/shiny-server/shaman/* /srv/shiny-server/ && \
+    rm -rf /srv/shiny-server/shaman && \
+    chown -R shiny.shiny  /srv/shiny-server/ && \
+    chown -R shiny.shiny  /opt/packman/ && \
+    rm /opt/shaman_package_201908.tar.gz && \
+    cp /srv/shiny-server/.Rprofile /srv/shiny-server/kronarshy/.Rprofile
+
+EXPOSE 3838
+
+EXPOSE 5438
+
+COPY docker_inst/shiny-server.sh /usr/bin/shiny-server.sh
+
+COPY docker_inst/run_kronarshy.R /usr/bin/run_kronarshy.R
+
+CMD ["/usr/bin/shiny-server.sh"] 

LoadPackages.R

@@ -9,11 +9,6 @@ if(!require(shiny)){
   library(shiny)
 }
 
-if(!require(shinydashboard)){
-  devtools::install_github('aghozlane/shinydashboard')
-  library(shinydashboard)
-}
-
 if(!require(rjson)){
   install.packages('rjson',  repos="https://cran.univ-paris1.fr/")
   library(rjson)
@@ -54,45 +49,12 @@ if (!require(circlize)) {
 }
 
 
-if (!require(devtools)) {
-  install.packages('devtools',  repos="https://cran.univ-paris1.fr/")
-  library(devtools)
-}
-if(!require(treeWeightD3)){
-   devtools::install_github('pierreLec/treeWeightD3')
-   library(treeWeightD3)
-}
 # if (!require(BiocInstaller)){
 #   source("https://bioconductor.org/biocLite.R")
 #   biocLite("BiocInstaller")
 #   library(BiocInstaller)
 # }
 
-#torename
-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(scatterD3)) {
-  #devtools::install_github('aghozlane/scatterD3')
-  install.packages("scatterD3", repos="https://cran.univ-paris1.fr/")
-  library(scatterD3)
-}
-
-if (!require(rNVD3)) {
-  devtools::install_github('aghozlane/rNVD3')
-  library(rNVD3)
-}
-
 if(!require(BiocManager)){
   install.packages("BiocManager")
 }
@@ -116,11 +78,6 @@ if (!require(shinyjs)) {
   library(shinyjs)
 }
 
-if(!require(d3vennR)){
-  devtools::install_github("timelyportfolio/d3vennR")
-  library(d3vennR)
-}
-
 if (!require(DT)) {
   install.packages('DT',  repos="https://cran.univ-paris1.fr/")
   library(DT)
@@ -136,11 +93,6 @@ if (!require(gplots)) {
   library(gplots)
 }
 
-if (!require(DESeq2shaman)) {
-  devtools::install_github("aghozlane/DESeq2shaman")
-  library(DESeq2shaman)
-}
-
 if (!require(ade4)) {
   install.packages('ade4',  repos="https://cran.univ-paris1.fr/")
   library(ade4)
@@ -161,16 +113,6 @@ if(!require(philentropy)){
   library(philentropy)
 }
 
-if(!require(PhyloTreeMetaR)){
-  devtools::install_github("pierreLec/PhyloTreeMetaR")
-  library(PhyloTreeMetaR)
-}
-
-if (!require("shinytoastr")){
-  devtools::install_github("mangothecat/shinytoastr")
-  library(shinytoastr)
-}
-
 if (!require("shinyWidgets")){
   install.packages("shinyWidgets")
   #devtools::install_github("aghozlane/shinyWidgets")
@@ -269,4 +211,63 @@ if(!require("igraph")){
 if(!require("visNetwork")){
   install.packages("visNetwork",  repos="https://cran.univ-paris1.fr/")
   library(visNetwork)
+}
+
+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("treeWeightD3")){
+  devtools::install_github('pierreLec/treeWeightD3')
+  library(treeWeightD3)
+}
+
+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("scatterD3")) {
+  #devtools::install_github('aghozlane/scatterD3')
+  install.packages("scatterD3", repos="https://cran.univ-paris1.fr/")
+  library(scatterD3)
+}
+
+if (!require("rNVD3")) {
+  devtools::install_github('aghozlane/rNVD3')
+  library(rNVD3)
+}
+
+if(!require("PhyloTreeMetaR")){
+  devtools::install_github("pierreLec/PhyloTreeMetaR")
+  library(PhyloTreeMetaR)
+}
+
+if (!require("shinytoastr")){
+  devtools::install_github("mangothecat/shinytoastr")
+  library(shinytoastr)
+}
+
+if(!require("d3vennR")){
+  devtools::install_github("timelyportfolio/d3vennR")
+  library(d3vennR)
+}
+
+if (!require("DESeq2shaman")) {
+  devtools::install_github("aghozlane/DESeq2shaman")
+  library(DESeq2shaman)
 }
\ No newline at end of file

Rfunctions/internal_masque.R

@@ -58,42 +58,42 @@ Project_box_result <- function(masque_key,curdir){
           br(),
           column(width=4,
                  h3("OTU building process"),
-                 shinydashboard::valueBox(ap$Count[1],tags$strong(tags$h5("Number of amplicons", style = "width: 70%;")), color = "light-blue", width = NULL, icon = uiOutput("amplicon_icon")),
-                 shinydashboard::valueBox(ap$Count[2],tags$strong(tags$h5("Remaining amplicons after dereplication", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("dereplication_icon")),
-                 shinydashboard::valueBox(ap$Count[3],tags$strong(tags$h5("Remaining amplicons after removing singletons", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("singleton_icon")),
-                 shinydashboard::valueBox(ap$Count[4],tags$strong(tags$h5("Remaining amplicons after removing chimera", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("chimera_icon")),
-                 shinydashboard::valueBox(ap$Count[5],tags$strong(tags$h5("Number of OTU", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("otu_icon"))
+                 shinydashboardshaman::valueBox(ap$Count[1],shiny::tags$strong(shiny::tags$h5("Number of amplicons", style = "width: 70%;")), color = "light-blue", width = NULL, icon = uiOutput("amplicon_icon")),
+                 shinydashboardshaman::valueBox(ap$Count[2],shiny::tags$strong(shiny::tags$h5("Remaining amplicons after dereplication", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("dereplication_icon")),
+                 shinydashboardshaman::valueBox(ap$Count[3],shiny::tags$strong(shiny::tags$h5("Remaining amplicons after removing singletons", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("singleton_icon")),
+                 shinydashboardshaman::valueBox(ap$Count[4],shiny::tags$strong(shiny::tags$h5("Remaining amplicons after removing chimera", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("chimera_icon")),
+                 shinydashboardshaman::valueBox(ap$Count[5],shiny::tags$strong(shiny::tags$h5("Number of OTU", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("otu_icon"))
           ),
           #column(width=5, div(img(src = "masque.png",width = "50%",height = "20%"))),
           if(json_data$type == "16S"){
             column(width=5,
                    strong(h3("16S annotation process")),
-                   shinydashboard::valueBox(ap$Count[6],tags$strong(tags$h5("Number of OTU annotated by SILVA", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("silva_icon")),
-                   shinydashboard::valueBox(ap$Count[7],tags$strong(tags$h5("Number of OTU annotated by Greengenes", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("greengenes_icon")),
-                   shinydashboard::valueBox(ap$Count[8],tags$strong(tags$h5("Number of OTU annotated by RDP", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("rdp_icon"))
+                   shinydashboardshaman::valueBox(ap$Count[6],shiny::tags$strong(shiny::tags$h5("Number of OTU annotated by SILVA", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("silva_icon")),
+                   shinydashboardshaman::valueBox(ap$Count[7],shiny::tags$strong(shiny::tags$h5("Number of OTU annotated by Greengenes", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("greengenes_icon")),
+                   shinydashboardshaman::valueBox(ap$Count[8],shiny::tags$strong(shiny::tags$h5("Number of OTU annotated by RDP", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("rdp_icon"))
             )
           }
           else if(json_data$type == "18S"){
             column(width=5,
                    strong(h3("18S annotation process")),
-                   shinydashboard::valueBox(ap$Count[6],tags$strong(tags$h5("Number of OTU annotated by SILVA", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("silva_icon")),
-                   shinydashboard::valueBox(ap$Count[7],tags$strong(tags$h5("Number of OTU annotated by RDP", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("rdp_icon"))
+                   shinydashboardshaman::valueBox(ap$Count[6],shiny::tags$strong(shiny::tags$h5("Number of OTU annotated by SILVA", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("silva_icon")),
+                   shinydashboardshaman::valueBox(ap$Count[7],shiny::tags$strong(shiny::tags$h5("Number of OTU annotated by RDP", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("rdp_icon"))
             )
           }
           else if(json_data$type == "23S_28S"){
             column(width=5,
                    strong(h3("23S/28S annotation process")),
-                   shinydashboard::valueBox(ap$Count[6],tags$strong(tags$h5("Number of OTU annotated by SILVA", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("silva_icon")),
-                   shinydashboard::valueBox(ap$Count[7],tags$strong(tags$h5("Number of OTU annotated by RDP", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("rdp_icon"))
+                   shinydashboardshaman::valueBox(ap$Count[6],shiny::tags$strong(shiny::tags$h5("Number of OTU annotated by SILVA", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("silva_icon")),
+                   shinydashboardshaman::valueBox(ap$Count[7],shiny::tags$strong(shiny::tags$h5("Number of OTU annotated by RDP", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("rdp_icon"))
             )
           }
           else{
             column(width=5,
                    strong(h3("ITS annotation process")),
-                   shinydashboard::valueBox(ap$Count[6],tags$strong(tags$h5("Number of OTU annotated by Unite", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("unite_icon")),
-                   shinydashboard::valueBox(ap$Count[7],tags$strong(tags$h5("Number of OTU annotated by Findley", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("findley_icon")),
-                   shinydashboard::valueBox(ap$Count[8],tags$strong(tags$h5("Number of OTU annotated by Underhill", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("underhill_icon")),
-                   shinydashboard::valueBox(ap$Count[9],tags$strong(tags$h5("Number of OTU annotated by RDP", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("rdp_icon"))
+                   shinydashboardshaman::valueBox(ap$Count[6],shiny::tags$strong(shiny::tags$h5("Number of OTU annotated by Unite", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("unite_icon")),
+                   shinydashboardshaman::valueBox(ap$Count[7],shiny::tags$strong(shiny::tags$h5("Number of OTU annotated by Findley", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("findley_icon")),
+                   shinydashboardshaman::valueBox(ap$Count[8],shiny::tags$strong(shiny::tags$h5("Number of OTU annotated by Underhill", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("underhill_icon")),
+                   shinydashboardshaman::valueBox(ap$Count[9],shiny::tags$strong(shiny::tags$h5("Number of OTU annotated by RDP", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("rdp_icon"))
             )
          },
          #offset = 4,
@@ -103,18 +103,18 @@ Project_box_result <- function(masque_key,curdir){
                     selectInput("masque_db","Select the database",choices=db_choices),
                     conditionalPanel(condition="input.masque_db=='rdp'",numericInput("rdp_thres",h6(strong("Threshold:")),0.5,step=0.01,min=0.01,max=1)),
                     actionButton("LoadResMasque", "Upload the results",icon=icon('upload')),
-                    tags$style(type='text/css', "#LoadResMasque { width:100%; }"),
+                    shiny::tags$style(type='text/css', "#LoadResMasque { width:100%; }")#,
                     #receiveSweetAlert(messageId = "LoadResMasque")
                 ),
-                #shinydashboard::box(title="Upload the results",width = NULL, background = "light-blue",
+                #shinydashboardshaman::box(title="Upload the results",width = NULL, background = "light-blue",
                 #selectInput("masque_database","Select the database",choices=c("Silva" = "silva","Greengenes" = "greengenes", "MARDE"="merde")),
-                #tags$style(type='text/css', "#masque_database { width:100%; margin-top: 5px;}"),
+                #shiny::tags$style(type='text/css', "#masque_database { width:100%; margin-top: 5px;}"),
                 #actionButton("RunResMasque",label = "Upload the results",icon=icon('upload')),
-                #tags$style(type='text/css', "#RunResMasque { width:100%; margin-top: 15px;}")
+                #shiny::tags$style(type='text/css', "#RunResMasque { width:100%; margin-top: 15px;}")
                 #),
                 box(id="box-zip",title="Download .zip file",width = NULL, status = "success",
                     downloadButton('Download_masque_zip', 'Download the results'),
-                    tags$style(type='text/css', "#Download_masque_zip { width:100%;}")
+                    shiny::tags$style(type='text/css', "#Download_masque_zip { width:100%;}")
                 )
          )
         )

docker_inst/.Rprofile

+library(packrat)
+packrat::init("/opt/packman/shaman/")

docker_inst/run_kronarshy.R

+library(packrat)
+packrat::init("/opt/packman/shaman/")
+library(shiny)
+runApp("/srv/shiny-server/kronarshy/", port=5438, host="0.0.0.0")
\ No newline at end of file

docker_inst/shiny-server.conf

+# Define the user we should use when spawning R Shiny processes
+run_as shiny;
+
+# Define a top-level server which will listen on a port
+server {
+  # Instruct this server to listen on port 80. The app at dokku-alt need expose PORT 80, or 500 e etc. See the docs
+  listen 80;
+
+  # Define the location available at the base URL
+  location / {
+
+    # Run this location in 'site_dir' mode, which hosts the entire directory
+    # tree at '/srv/shiny-server'
+    site_dir /srv/shiny-server;
+    
+    # Define where we should put the log files for this location
+    log_dir /var/log/shiny-server;
+    
+    # Should we list the contents of a (non-Shiny-App) directory when the user 
+    # visits the corresponding URL?
+    #directory_index on;
+  }
+}
+
+# Define a top-level server which will listen on a port                          
+server {                                                                         
+  # Instruct this server to listen on port 80. The app at dokku-alt need expose PORT 80, or 500 e etc. See the docs
+  listen 5438;                                                                     
+                                                                                 
+  # Define the location available at the base URL                                
+  location / {                                                                   
+                                                                                 
+    # Run this location in 'site_dir' mode, which hosts the entire directory     
+    # tree at '/srv/shiny-server'                                                
+    site_dir /srv/shiny-server/kronarshy;                                                  
+                                                                                 
+    # Define where we should put the log files for this location                 
+    log_dir /var/log/shiny-server/kronarshy;                                               
+                                                                                 
+    # Should we list the contents of a (non-Shiny-App) directory when the user   
+    # visits the corresponding URL?                                              
+    #directory_index on;                                                          
+  }                                                                              
+}

docker_inst/shiny-server.sh

+#!/bin/sh
+mkdir -p /srv/shiny-server/www/masque/todo /srv/shiny-server/www/masque/doing /srv/shiny-server/www/masque/error /srv/shiny-server/www/masque/done
+chown shiny.shiny /srv/shiny-server/www/masque/todo /srv/shiny-server/www/masque/doing /srv/shiny-server/www/masque/error /srv/shiny-server/www/masque/done
+exec nohup /usr/bin/python3 /usr/bin/shaman_bioblend/shaman_bioblend.py  -w /srv/shiny-server/www/masque/ -s -d &
+
+# Make sure the directory for individual app logs exists
+mkdir -p /var/log/shiny-server
+chown shiny.shiny /var/log/shiny-server
+
+exec shiny-server >> /var/log/shiny-server.log 2>&1
+
+exec nohup /usr/bin/Rscript /usr/bin/run_kronarshy.R&

server.R

@@ -457,13 +457,13 @@ shinyServer(function(input, output,session) {
     data = tmp$data
     check = tmp$check
     cond = (!is.null(data$counts) && nrow(data$counts)>0 && !is.null(data$taxo) && nrow(data$taxo)>0)
-    res = shinydashboard::valueBox(paste0(0, "%"),h6(strong("Annotated features")), color = "light-blue",width=NULL,icon = icon("list"))
+    res = shinydashboardshaman::valueBox(paste0(0, "%"),h6(strong("Annotated features")), color = "light-blue",width=NULL,icon = icon("list"))
     
     if(cond)
     {
       percent = round(100*tmp$percent,2)
-      if(percent==0) res = shinydashboard::valueBox(paste0(percent, "%"),h6(strong("Annotated features")), color = "red",width=NULL,icon = icon("list"))  
-      if(percent!=0) res = shinydashboard::valueBox(paste0(percent, "%"),h6(strong("Annotated features")), color = "green",width=NULL,icon = icon("list"))  
+      if(percent==0) res = shinydashboardshaman::valueBox(paste0(percent, "%"),h6(strong("Annotated features")), color = "red",width=NULL,icon = icon("list"))  
+      if(percent!=0) res = shinydashboardshaman::valueBox(paste0(percent, "%"),h6(strong("Annotated features")), color = "green",width=NULL,icon = icon("list"))  
       
     }
     
@@ -1203,12 +1203,12 @@ shinyServer(function(input, output,session) {
     res = NULL
     error_progress = values$error_progress
     num = round(as.numeric(values$num),1)
-    res = shinydashboard::valueBox("0 %",h6(strong("Waiting for the data...")), color = "light-blue",width=NULL,icon = uiOutput("spinner_icon"))  
+    res = shinydashboardshaman::valueBox("0 %",h6(strong("Waiting for the data...")), color = "light-blue",width=NULL,icon = uiOutput("spinner_icon"))  
     CMP = isolate(CheckMasque(input, values, check_mail=FALSE))
     Error = CMP$Error
-    if(num>=100) res = shinydashboard::valueBox(paste("100 %"),h6(strong("Analysis completed ! Check your mail.")), color = "green",width=NULL,icon =  uiOutput("check_icon"))
-    else if(is.null(Error) || num>=1) res = shinydashboard::valueBox(paste(values$num,"%"),h6(strong("Analysis in progress...")), color = "green",width=NULL,icon = uiOutput("spinner_anim"))  
-    else if(!is.null(Error) && num>=1 || error_progress) res = shinydashboard::valueBox(paste(values$num,"%"),h6(strong("Workflow failed during progression...")), color = "red",width=NULL,icon = uiOutput("spinner_anim"))  
+    if(num>=100) res = shinydashboardshaman::valueBox(paste("100 %"),h6(strong("Analysis completed ! Check your mail.")), color = "green",width=NULL,icon =  uiOutput("check_icon"))
+    else if(is.null(Error) || num>=1) res = shinydashboardshaman::valueBox(paste(values$num,"%"),h6(strong("Analysis in progress...")), color = "green",width=NULL,icon = uiOutput("spinner_anim"))  
+    else if(!is.null(Error) && num>=1 || error_progress) res = shinydashboardshaman::valueBox(paste(values$num,"%"),h6(strong("Workflow failed during progression...")), color = "red",width=NULL,icon = uiOutput("spinner_anim"))  
     return(res)
   })
   
@@ -2093,11 +2093,11 @@ shinyServer(function(input, output,session) {
       #### Ajout fontion check target
       #infoBox(h6(strong("Target file")), subtitle = h6("Your target file is OK"), icon = icon("thumbs-o-up"),color = "green",width=NULL,fill=TRUE)
       labeled = round(labeled,2)
-      if(labeled>0) res = shinydashboard::valueBox(paste0(labeled, "%"),h6(strong("Labeled features")), color = "green",width=NULL,icon = icon("list"))
-      else res = shinydashboard::valueBox(paste0(labeled, "%"),h6(strong("Labeled features")), color = "red",width=NULL,icon = icon("list"))  
+      if(labeled>0) res = shinydashboardshaman::valueBox(paste0(labeled, "%"),h6(strong("Labeled features")), color = "green",width=NULL,icon = icon("list"))
+      else res = shinydashboardshaman::valueBox(paste0(labeled, "%"),h6(strong("Labeled features")), color = "red",width=NULL,icon = icon("list"))  
     }
     #else infoBox(h6(strong("Target file")), subtitle = h6("Label of the target file must correspond to count table column names") ,color = "light-blue",width=NULL,fill=TRUE, icon = icon("warning"))
-    else res = shinydashboard::valueBox(paste0(0, "%"),h6(strong("Labeled features")), color = "light-blue",width=NULL,icon = icon("list"))
+    else res = shinydashboardshaman::valueBox(paste0(0, "%"),h6(strong("Labeled features")), color = "light-blue",width=NULL,icon = icon("list"))
     return(res)
   }
   )