Commit 5d520be3 authored by Amine  GHOZLANE's avatar Amine GHOZLANE
Browse files

Update documentation and dockerfile

parent 30143655
Pipeline #13917 passed with stage
in 45 minutes and 30 seconds
......@@ -46,20 +46,19 @@ RUN R -e """install.packages('packrat', repos='http://cran.univ-paris1.fr/');lib
COPY docker_inst/shiny-server.conf /etc/shiny-server/shiny-server.conf
COPY docker_inst/.Rprofile /srv/shiny-server/
COPY . /srv/shiny-server/
COPY docker_inst/shiny-server.sh /usr/bin/shiny-server.sh
COPY docker_inst/run_kronarshy.R /usr/bin/run_kronarshy.R
RUN 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 && \
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
cp /srv/shiny-server/.Rprofile /srv/shiny-server/kronarshy/.Rprofile && \
chmod +x /usr/bin/shiny-server.sh
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"]
......@@ -228,30 +228,25 @@ function(request) {
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=3.6.1. Packrat framework allow an easy installation of all the dependencies. First, install R 3.1.2 as local install as follow:",style = "font-family: 'times'; font-si16pt"),
mainPanel(div(style = 'max-width: 900px; word-wrap: break-word;',"# Install R 3.6.1", 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/",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_20190809.tar.gz"),width=9,class="mainwell"),
p("Of note, raw data submission is not possible with this version. Then, you can install SHAMAN with packrat:"),
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 SHAMAN package",br(),"wget ftp://shiny01.hosting.pasteur.fr/pub/shaman_20190809.tar.gz", br(),
"# Install SHAMAN dependencies",br(),
"mkdir /some/location/shaman", br(), "/some/location/r_bin/bin/R",br(),
"install.packages(\"packrat\")",br(),"packrat::unbundle(\"shaman_20190809.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')"),width=9,class="mainwell")),
"# Download packrat package",br(),"wget ftp://shiny01.hosting.pasteur.fr/pub/shaman_package_201908.tar.gz", br(),
"mkdir packrat/shaman"), width=9,class="mainwell"),
p("Now you can run R:"),
mainPanel(div(style = 'max-width: 900px; word-wrap: break-word;',
"install.packages(c(\"packrat\", \"shiny\"))",br(),
"packrat::unbundle(\"shaman_package_201908.tar.gz\", \"packrat/shaman\")", 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",
p("SHAMAN is available for R=3.6.1. 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"),
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')"),width=9,class="mainwell"),
"if(!require('shiny')){",br()," install.packages('shiny')",br(),"}",br(),
"system(\"Rscript -e '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(),
"shiny::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 :"),
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")))
......
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