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Commit 62b4a71a authored by Amine GHOZLANE's avatar Amine GHOZLANE
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Update guide and redesign shape of download/install part

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ui.R
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function(request) {
sidebar <- dashboardSidebar(
useShinyjs(),
includeCSS("www/custom_shaman.css"),
inlineCSS(appCSS),
# tags$head(
# tags$script(src = "custom.js")
......@@ -215,37 +216,39 @@ 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 = 'max-width: 900px',"docker pull aghozlane/shaman && docker run --rm -p 80:80 -p 5438:5438 aghozlane/shaman")),
mainPanel(div(style = 'max-width: 900px',"docker pull aghozlane/shaman && docker run --rm -p 80:80 -p 5438:5438 aghozlane/shaman"),width=8,class="mainwell"),
p("Then connect to http://0.0.0.0/ with your favorite web navigator."),
p("Failed: port is already allocated ?"),
wellPanel(div(style = 'max-width: 900px',"docker run --rm -p 3838:80 -p 5438:5438 aghozlane/shaman")),
mainPanel(div(style = 'max-width: 900px',"docker run --rm -p 3838:80 -p 5438:5438 aghozlane/shaman"),width=6,class="mainwell"),
p("Then connect to http://0.0.0.0:3838/."),
p("- Docker update after an update of SHAMAN:"),
wellPanel(div(style = 'max-width: 900px',"docker pull aghozlane/shaman"))
mainPanel(div(style = 'max-width: 900px',"docker pull aghozlane/shaman"),width=4,class="mainwell")
),
tabPanel("R install with Packrat",
p("SHAMAN is available for R=3.1.2. Packrat framework installation allow an easy installation of all the dependencies. Of note, raw data submission is not possible with this version. First, install R 3.1.2 as local install as follow:",style = "font-family: 'times'; font-si16pt"),
wellPanel(style = 'width: 150%; word-wrap: break-word;',"# Install R 3.1.2", br(),
mainPanel(div(style = 'max-width: 900px; word-wrap: break-word;',"# Install R 3.1.2", br(),
"wget https://pbil.univ-lyon1.fr/CRAN/src/base/R-3/R-3.1.2.tar.gz && tar -zxf R-3.1.2.tar.gz",br(),"mkdir /some/location/r_bin",br(),
"cd R-3.1.2/ && ./configure --prefix=/some/location/r_bin/ && make && make install && /some/location/r_bin/bin/R", br(),
"# Download SHAMAN package",br(),"wget ftp://shiny01.hosting.pasteur.fr/pub/shaman_package.tar.gz"), br(),
p("This installation will not interact with other R installation. Then, you can install shaman with packrat:", a("here", target="_blank", href="shamanapp.R"), "and executed as following :"),
wellPanel(style = 'width: 150%; word-wrap: break-word;',"# Install SHAMAN dependencies",br(),
"cd R-3.1.2/",br(), "./configure --prefix=/some/location/r_bin/", br(), "make && make install", br(), "/some/location/r_bin/bin/R", br(),
"install.packages(c('devtools', 'codetools', 'lattice', 'MASS', 'survival', 'packrat'))", br(),
"library(devtools)",br(),"devtools::install_github(c('aghozlane/nlme'))", br(),
"# Download SHAMAN package",br(),"wget ftp://shiny01.hosting.pasteur.fr/pub/shaman_package.tar.gz"),width=9,class="mainwell"),
p("This installation will not interact with other R installation. Then, you can install SHAMAN with packrat:"),
mainPanel(div(style = 'max-width: 900px; word-wrap: break-word;',"# Install SHAMAN dependencies",br(),
"mkdir /some/location/shaman", br(), "/some/location/r_bin/bin/R",br(),
"install.packages(\"packrat\")",br(),"packrat::unbundle(\"shaman_package.tar.gz\", \"/packrat/location/shaman\")"),
p("Now you can run SHAMAN:"),
wellPanel(style = 'width: 50%; word-wrap: break-word;',"library(packrat)",br(),"packrat::init(\"/packrat/location/shaman\")",br(),"library(shiny)",br(),
"install.packages(\"packrat\")",br(),"packrat::unbundle(\"shaman_package.tar.gz\", \"/packrat/location/shaman\")"), width=9,class="mainwell"),
p("Now you can run SHAMAN:"),
mainPanel(div(style = 'max-width: 900px; word-wrap: break-word;',"library(packrat)",br(),"packrat::init(\"/packrat/location/shaman\")",br(),"library(shiny)",br(),
"system(\"Rscript -e 'library(\\\"shiny\\\");runGitHub(\\\"pierreLec/KronaRShy\\\",port=5438)'\",wait=FALSE)",
br(),"runGitHub('aghozlane/shaman')")),
br(),"runGitHub('aghozlane/shaman')"),width=9,class="mainwell")),
tabPanel("R install (DEPRECATED)",
p("SHAMAN is available for R=3.1.2. 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"),
wellPanel(style = 'width: 50%; word-wrap: break-word;',"# Load shiny packages",br(),
mainPanel(div(style = 'max-width: 900px; word-wrap: break-word;',"# Load shiny packages",br(),
"if(!require('shiny')){",br()," install.packages('shiny')",br()," library(shiny)",br(),"}",br(),
"system(\"Rscript -e 'library(\\\"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(),"runGitHub('aghozlane/shaman')"),
br(),"# Install dependencies,",br(),"# download last version from github,",br(),"# and run SHAMAN in one command:",br(),"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 :"),
wellPanel(style = 'width: 50%; word-wrap: break-word;',"chmod +x ./shamanapp.R && Rscript ./shamanapp.R"),br(),
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")))
)
......
www/Userguide.pdf
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