Fix for rNVD3shaman for docker install

Dockerfile

 FROM ubuntu:18.04
-ARG SOURCE_VERSION=202007
+ARG SOURCE_VERSION=202009
 MAINTAINER Amine Ghozlane "amine.ghozlane@pasteur.fr"
 
 RUN apt-get update && apt-get install -y \
@@ -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_${SOURCE_VERSION}.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_${SOURCE_VERSION}.tar.gz', '/opt/packman')"""
+RUN R -e """install.packages('devtools', repos='http://cran.univ-paris1.fr/');devtools::install_github('rstudio/packrat');packrat::unbundle('/opt/shaman_package_${SOURCE_VERSION}.tar.gz', '/opt/packman')"""
 
 COPY docker_inst/shiny-server.conf  /etc/shiny-server/shiny-server.conf
 COPY docker_inst/.Rprofile  /srv/shiny-server/

README.md

@@ -25,61 +25,62 @@ Hereafter is the global workflow of the SHAMAN application:
 
 SHAMAN is available for R 3.6.1. Here are different ways to install the application:
 
-### R install
+### Docker install
 
-R install will require Gfortran on mac (https://cran.r-project.org/bin/macosx/tools/) and Rtools on windows (https://cran.r-project.org/bin/windows/Rtools/index.html). 
-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 :
-```
-# Load shiny packages
-if(!require('shiny')){
- install.packages('shiny')
- library(shiny)
-}
+Docker install is the easiest way to use SHAMAN locally. First, install docker:
+- Install docker on ubuntu (Linux): https://docs.docker.com/engine/installation/linux/ubuntulinux/
+- Install docker on Windows and Mac: https://www.docker.com/
 
-# Install dependencies, download last version of SHAMAN from github and run shaman in one command :
-runGitHub('aghozlane/shaman')
+Now in your terminal:
 ```
-This script can also be executed as following : 
+docker pull aghozlane/shaman && docker run --rm -p 80:80 -p 5438:5438 aghozlane/shaman
 ```
-chmod +x ./shaman/www/shaman.R && Rscript ./shaman/www/shaman.R
+Then connect to http://0.0.0.0/ with your favorite web navigator.
+Failed: port is already allocated ?
+```
+docker run --rm -p 3838:80 -p 5438:5438 aghozlane/shaman
+```
+Then connect to http://0.0.0.0:3838/.
+Docker update after an update of SHAMAN:
+```
+docker pull aghozlane/shaman
 ```
-
 
 ### R install with packrat (linux only)
 
 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.
 ```
 # Download packrat package
-wget ftp://shiny01.hosting.pasteur.fr/pub/shaman_package_202007.tar.gz
-mkdir packrat/shaman
+wget ftp://shiny01.hosting.pasteur.fr/pub/shaman_package_202009.tar.gz
+mkdir packrat/
 ```
 Now you can run R:
 ```
-install.packages("packrat")
-packrat::unbundle("shaman_package_202007.tar.gz", "packrat/shaman")
+install.packages("devtools")
+devtools::install_github("rstudio/packrat")
+packrat::unbundle("shaman_package_202009.tar.gz", "packrat/")
 packrat::init("packrat/shaman")
 system("Rscript -e 'shiny::runGitHub("pierreLec/KronaRShy",port=5438)'",wait=FALSE),
 shiny::runGitHub('aghozlane/shaman')
 ```
-### Docker install
 
-Docker install is the easiest way to use SHAMAN locally. First, install docker:
-- Install docker on ubuntu (Linux): https://docs.docker.com/engine/installation/linux/ubuntulinux/
-- Install docker on Windows and Mac: https://www.docker.com/
+### R install (deprecated)
 
-Now in your terminal:
-```
-docker pull aghozlane/shaman && docker run --rm -p 80:80 -p 5438:5438 aghozlane/shaman
-```
-Then connect to http://0.0.0.0/ with your favorite web navigator.
-Failed: port is already allocated ?
+R install will require Gfortran on mac (https://cran.r-project.org/bin/macosx/tools/) and Rtools on windows (https://cran.r-project.org/bin/windows/Rtools/index.html). 
+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 :
 ```
-docker run --rm -p 3838:80 -p 5438:5438 aghozlane/shaman
+# Load shiny packages
+if(!require('shiny')){
+ install.packages('shiny')
+ library(shiny)
+}
+
+# Install dependencies, download last version of SHAMAN from github and run shaman in one command :
+runGitHub('aghozlane/shaman')
 ```
-Then connect to http://0.0.0.0:3838/.
-Docker update after an update of SHAMAN:
+This script can also be executed as following : 
 ```
-docker pull aghozlane/shaman
+chmod +x ./shaman/www/shaman.R && Rscript ./shaman/www/shaman.R
 ```
 
 ### CONDA

ui.R

@@ -227,17 +227,18 @@ function(request) {
                                     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"),
                                              mainPanel(div(style = 'max-width: 900px; word-wrap: break-word;',
-                                                           "# Download packrat package",br(),"wget ftp://shiny01.hosting.pasteur.fr/pub/shaman_package_201909.tar.gz", br(),
-                                                           "mkdir packrat/shaman"), width=9,class="mainwell"),
+                                                           "# Download packrat package",br(),"wget ftp://shiny01.hosting.pasteur.fr/pub/shaman_package_202009.tar.gz", br(),
+                                                           "mkdir packrat/"), width=9,class="mainwell"),
                                              p("Now you can run R:"),
                                              mainPanel(div(style = 'max-width: 900px; word-wrap: break-word;',
-                                                           "install.packages(\"packrat\")",br(),
-                                                           "packrat::unbundle(\"shaman_package_201909.tar.gz\", \"packrat/shaman\")", br(),
+                                                           "install.packages(\"devtools\")",br(),
+                                                           "devtools::install_github(\"rstudio/packrat\")",br(),
+                                                           "packrat::unbundle(\"shaman_package_202009.tar.gz\", \"packrat/\")", br(),
                                                            "packrat::init(\"packrat/shaman\")",br(),
                                                            "system(\"Rscript -e 'shiny::runGitHub(\\\"pierreLec/KronaRShy\\\",port=5438)'\",wait=FALSE)",
                                                            br(),"shiny::runGitHub('aghozlane/shaman')"),width=9,class="mainwell")),
                                     
-                                    tabPanel("R install",
+                                    tabPanel("R install (deprecated)",
                                              p("SHAMAN is available for R=3.6.1. Gfortran is required on mac (https://cran.r-project.org/bin/macosx/tools/) and Rtools on windows (https://cran.r-project.org/bin/windows/Rtools/index.html). 
                                              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"),