CONNECTOR - How to install

CONNECTOR

it is built under R 4.1.0, for previous versions we suggest installing the right version of the package locfit:

install_version("locfit", version = "1.5-9.2")

Note that R should be built with tcltk support. To check this, you should run capabilities(“tcltk”) from R. If it returns FALSE then we suggest checking how to cope with this from here.

Before installing CONNECTOR, the following R packages have to be installed:

install.packages(c('cowplot', 'fda', 'flexclust','ggplot2', 'MASS',
                   'Matrix', 'plyr','ggplotify', 'RColorBrewer',
                   'readxl', 'reshape2', 'splines', 'statmod', 
                   'sfsmisc','shinyWidgets', 'viridis', 'dashboardthemes',
                   'shinybusy','shinydashboard','shinyjs','tidyr',
                   'shinyFiles','devtools'))"

Finally, to install CONNECTOR you can use the devtools R package:

library(devtools)
install_github("https://github.com/qBioTurin/connector", ref="master")

Here the CONNECTOR step by step guide: CONNECTOR pdf.

Docker

If you want to use Docker (which is not mandatory), you need to have it installed on your machine. For more info see this document: https://docs.docker.com/engine/installation/.

How to install docker

Ensure your user has the rights to run docker (without the use of sudo). To create the docker group and add your user:

Create the docker group.

  $ sudo groupadd docker

Add your user to the docker group.

  $ sudo usermod -aG docker $USER

Log out and log back in so that your group membership is re-evaluated.

How to run CONNECTOR from docker

Without installing CONNECTOR:

Download the image from dockerhub

  $ docker pull qbioturin/connector:latest

Run the RStudio Docker image with CONNECTOR installed and work with RStudio in the browser

  $ docker run --cidfile=dockerID -e DISABLE_AUTH=true -p 8787:8787 -d qbioturin/connector:latest
  $ open http://localhost:8787/

From CONNECTOR: it is possible to download and run the RStudio Docker image by using the CONNECTOR functions called downloadContainers and docker.run as follows:
```
 > downloadContainers()
 > docker.run()
```