Commit ae981ac2 authored by Amine  GHOZLANE's avatar Amine GHOZLANE

Update treeweight and resolve export table

parent 663d1592
Pipeline #14746 failed with stage
in 4 minutes and 2 seconds
...@@ -4,3 +4,4 @@ ...@@ -4,3 +4,4 @@
.DS_Store .DS_Store
.Rproj.user .Rproj.user
www/masque.png www/masque.png
www/Workflow_sh_old.png
...@@ -41,7 +41,7 @@ RUN wget --no-verbose https://cran.r-project.org/src/base/R-3/R-3.6.1.tar.gz -P ...@@ -41,7 +41,7 @@ RUN wget --no-verbose https://cran.r-project.org/src/base/R-3/R-3.6.1.tar.gz -P
wget ftp://shiny01.hosting.pasteur.fr/pub/shaman_package_201908.tar.gz -P /opt && \ wget ftp://shiny01.hosting.pasteur.fr/pub/shaman_package_201908.tar.gz -P /opt && \
mkdir /opt/packman 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')""" RUN R -e """install.packages('packrat', repos='http://cran.univ-paris1.fr/');library("packrat");packrat::unbundle('/opt/shaman_package_201909.tar.gz', '/opt/packman')"""
COPY docker_inst/shiny-server.conf /etc/shiny-server/shiny-server.conf COPY docker_inst/shiny-server.conf /etc/shiny-server/shiny-server.conf
COPY docker_inst/.Rprofile /srv/shiny-server/ COPY docker_inst/.Rprofile /srv/shiny-server/
......
...@@ -3121,7 +3121,7 @@ shinyServer(function(input, output,session) { ...@@ -3121,7 +3121,7 @@ shinyServer(function(input, output,session) {
## Export Distancetable in .csv ## Export Distancetable in .csv
output$ExportDistancetable <- downloadHandler( output$ExportDistancetable <- downloadHandler(
filename = function() { filename = function() {
if(input$sepdiversity=="\t") 'SHAMAN_Distance.tsv' if(input$sepdistance=="\t") 'SHAMAN_Distance.tsv'
else 'SHAMAN_Distance.csv' else 'SHAMAN_Distance.csv'
}, },
content = function(file){ content = function(file){
...@@ -3129,7 +3129,7 @@ shinyServer(function(input, output,session) { ...@@ -3129,7 +3129,7 @@ shinyServer(function(input, output,session) {
## Phylogenetic tree ## Phylogenetic tree
tree = dataInputTree()$data tree = dataInputTree()$data
tmp = as.matrix(Plot_diag_pcoaEigen(input,resDiff,tree)$dataDiv) tmp = as.matrix(Plot_diag_pcoaEigen(input,resDiff,tree)$dataDiv)
datatable(tmp,rownames= FALSE) #datatable(tmp,rownames= FALSE)
write.table(tmp, file,row.names = FALSE, sep=input$sepdistance) write.table(tmp, file,row.names = FALSE, sep=input$sepdistance)
}) })
...@@ -3843,7 +3843,7 @@ shinyServer(function(input, output,session) { ...@@ -3843,7 +3843,7 @@ shinyServer(function(input, output,session) {
resDiff = ResDiffAnal() resDiff = ResDiffAnal()
tmp = Plot_Visu_Diversity(input,resDiff)$dataDiv tmp = Plot_Visu_Diversity(input,resDiff)$dataDiv
tmp$VarX=NULL; tmp$VarCol=NULL tmp$VarX=NULL; tmp$VarCol=NULL
datatable(tmp[,c(4,5,1,2,3)],rownames= FALSE) #datatable(tmp[,c(4,5,1,2,3)],rownames= FALSE)
write.table(tmp, file,row.names = FALSE, sep=input$sepdiversity) write.table(tmp, file,row.names = FALSE, sep=input$sepdiversity)
} }
) )
......
...@@ -225,7 +225,7 @@ function(request) { ...@@ -225,7 +225,7 @@ function(request) {
tabPanel("R install with Packrat (linux only)", tabPanel("R install with Packrat (linux only)",
p("SHAMAN is available for R=3.6.1. Packrat framework allows an easy installation of all the dependencies. Of note, raw data submission is not possible with this version.",style = "font-family: 'times'; font-si16pt"), p("SHAMAN is available for R=3.6.1. Packrat framework allows an easy installation of all the dependencies. Of note, raw data submission is not possible with this version.",style = "font-family: 'times'; font-si16pt"),
mainPanel(div(style = 'max-width: 900px; word-wrap: break-word;', mainPanel(div(style = 'max-width: 900px; word-wrap: break-word;',
"# Download packrat package",br(),"wget ftp://shiny01.hosting.pasteur.fr/pub/shaman_package_201908.tar.gz", br(), "# Download packrat package",br(),"wget ftp://shiny01.hosting.pasteur.fr/pub/shaman_package_201909.tar.gz", br(),
"mkdir packrat/shaman"), width=9,class="mainwell"), "mkdir packrat/shaman"), width=9,class="mainwell"),
p("Now you can run R:"), p("Now you can run R:"),
mainPanel(div(style = 'max-width: 900px; word-wrap: break-word;', mainPanel(div(style = 'max-width: 900px; word-wrap: break-word;',
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment