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')"""
@@ -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 :
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.
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 :
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. 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"),