Commit d776df51 authored by svolant's avatar svolant
Browse files

Merge branch 'master' of https://projets.pasteur.fr/git/meta16s

parents 9ed59fee 4bd682bb
......@@ -130,7 +130,10 @@ if (!require(scales)) {
install.packages('scales')
library(scales)
}
# if(!require(plotly)){
# install.packages("plotly")
# library(plotly)
# }
# Allow to upload 50M files only shaman server
if(Sys.info()["nodename"] == "shaman"){
......
......@@ -316,7 +316,7 @@ GetCountsMerge <- function(input,dataInput,taxoSelect,target,design)
## Create the dds object
dds <- DESeqDataSetFromMatrix(countData=CT, colData=target, design=design,ignoreRank=TRUE)
save(dds,file="testdds.RData")
#save(dds,file="testdds.RData")
if(is.null(VarNorm)){
## Counts normalisation
## Normalisation with or without 0
......
source('LoadPackages.R')
if(!require(plotly)){
install.packages("plotly")
library(plotly)
}
shinyServer(function(input, output,session) {
hide(id = "loading-content", anim = TRUE, animType = "fade",time=1.5)
......@@ -296,7 +293,7 @@ shinyServer(function(input, output,session) {
res = NULL
counts = isolate(dataMergeCounts()$counts)
tot = rowSums(counts)
save(counts,tot,file="testFilter.RData")
#save(counts,tot,file="testFilter.RData")
withProgress({tmp = SelectThreshAb(counts,lambda=max(round(sum(counts)/nrow(counts)*0.05),min(tot)+1),graph=FALSE)},message="Loading...")
res = sliderInput("SliderThAb","Threshold on the total abundance (in log)",min=0,max=round(max(log(tot+1)),1),value = log(tmp+1))
......
......@@ -25,10 +25,6 @@ if(!require(shinyjs)){
install.packages("shinyjs")
library(shinyjs)
}
if(!require(plotly)){
install.packages("plotly")
library(plotly)
}
function(request) {
sidebar <- dashboardSidebar(
......@@ -221,7 +217,7 @@ body <- dashboardBody(
"Then, you will need to install the", a("Docker toolbox.", href="https://www.docker.com/products/docker-toolbox"),
"Once installed, run ‘Docker Quickstart Terminal’ application."),
p("- Running SHAMAN:"),
wellPanel(div(style = 'width: 400px',"docker run --rm -p 80:80 aghozlane/shaman")),
wellPanel(div(style = 'width: 400px',"docker pull aghozlane/shaman && docker run --rm -p 80:80 aghozlane/shaman")),
p("Then connect to http://0.0.0.0/ with your favorite web navigator."),
p("Failed: port is already allocated ?"),
wellPanel(div(style = 'width: 400px',"docker run --rm -p 3838:80 aghozlane/shaman")),
......
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