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:
...
@@ -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:
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).
Docker install is the easiest way to use SHAMAN locally. First, install docker:
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 :
- Install docker on ubuntu (Linux): https://docs.docker.com/engine/installation/linux/ubuntulinux/
```
- Install docker on Windows and Mac: https://www.docker.com/
# 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 :
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)
### 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.
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.
Docker install is the easiest way to use SHAMAN locally. First, install docker:
### R install (deprecated)
- Install docker on ubuntu (Linux): https://docs.docker.com/engine/installation/linux/ubuntulinux/
- Install docker on Windows and Mac: https://www.docker.com/
Now in your terminal:
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 :
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"),
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).
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.
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"),
The installation, download and execution can all be performed with a small R script:",style="font-family: 'times'; font-si16pt"),