dockerflow - Docker-compose setup for simultaneous running of the flowcatchR-based containers

Introduction

This repository provides the docker-compose.yml configuration file for running the flowcatchR-based containers simultaneously on the same machine using Docker containers and Docker Compose.

The components are:

• flowstudio - https://github.com/federicomarini/flowstudio, a command-line/IDE interface to RStudio where flowcatchR and its dependencies are preinstalled.
• flowshiny - https://github.com/federicomarini/flowshiny, a Shiny Server running the shinyFlow web application
• flowjupy - https://github.com/federicomarini/flowjupy, a Jupyter Notebook interface

For more information on how to install the single components, please refer to their repositories.

Installation and setup

This app needs a recent version of Docker and Docker Compose:

• Docker installation instructions
• Docker Compose installation instructions
• clone this repository (git clone https://github.com/federicomarini/dockerflow.git)

Usage

• cd into the dockerflow folder
• docker-compose up (to pull the Docker images from the DockerHub)
• ... or alternatively docker-compose up --file docker-compose_DIY.yml (to have the images built locally from the cloned repositories of the components)
• If all goes well
  • On Linux, browse to http://localhost:8888 for the Jupyter notebook interface available in the home folder to find example notebooks illustrating the usage of the flowcatchR package
  • On Linux, browse to http://localhost:3838/shinyFlow for the shiny web application illustrating the usage of the flowcatchR package
  • On Linux, browse to http://localhost:8787 for the RStudio IDE interface available, , after logging in with user rstudio and password rstudio. A sample script with the full steps of the workflow is available for the user to learn and explore the functionality of the flowcatchR package. The package can be loaded with the conventional library("flowcatchR") command
  • On MacOS or Windows running Docker Toolbox find the Docker host URL with docker-machine ip default|[name of the virtual machine] and replace localhost in the locations specified above with the returned IP address

Contact

For additional details regarding the functions of flowcatchR, please consult the package documentation, the package vignette or write an email to marinif@uni-mainz.de.

Bug reports/Issues/New features

Please use https://github.com/federicomarini/flowcatchR/issues for reporting bugs, issues or for suggesting new features to be implemented.