kamermanpr/docker-pangolin-circadian repository overview

⁠docker-pangolin-circadian

A dockerfile to create an image of the R environment required to run the 'pangolin-circadian' data analysis scripts (kamermanpr/pangolin-circadian⁠).

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⁠R environment

The image is built using the rocker/verse⁠ image of base R⁠ v3.5.2, and includes RStudio server⁠, the TinyTex⁠ Latex distribution, the tidyverse⁠ suite of R packages (with dependencies), and several R packages (with dependencies) that are required to run the markdown scripts in pangolin-circadian⁠. CRAN packages were installed from MRAN⁠ using the lasted package releases at the time the image was generated.

⁠Details

• OS:
  • Debian:stretch
• R:
  • v3.5.2
• RStudio server:
  • v1.1.456
• MRAN packages:
  • magrittr'
  • ggfortify'
  • readxl
  • knitr
  • skimr
  • boot
  • ggridges
  • lubridate
  • multitaper
  • zoo
  • tidyquant
  • patchwork
  • ggforce
  • lmerTest
  • robustlmm
  • sjPlot'
• LaTex:
  • TinyTex

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⁠Using Docker to run the pangolin-circadian analysis

You need to have Docker installed on your computer. To do so, go to docker.com⁠ and follow the instructions for downloading and installing Docker for your operating system. Once Docker has been installed, follow the steps below, noting that Docker commands are entered in a terminal window (Linux and OSX/macOS) or command prompt window (Windows). Windows users also may wish to install GNU Make⁠ (required for the make method of running the scripts) and Git⁠ version control software (not essential).

⁠Download the latest image

Enter: docker pull kamermanpr/docker-pangolin-circadian:v1.0.0

⁠Run the container

Enter: docker run -d -p 8787:8787 --name pangolin -e USER=user -e PASSWORD=password kamermanpr/docker-pangolin-circadian:v1.0.0

⁠Login to RStudio Server

• Open a web browser window and navigate to: localhost:8787

• Use the following login credentials:

  • Username: user
  • Password: password

⁠Prepare the pain-threshold directory

clone the (kamermanpr/pangolin-circadian⁠ repo from GitHub: git clone https://github.com/kamermanpr/pangolin-circadian), or download the zip file from figshare (DOI: 10.6084/m9.figshare.7928084⁠), and upload it to RStudio server (it will automatically unzip).

The pangolin-circadian directory comes with the outputs for all the analysis scripts in the /outputs directory (html and md formats). However, should you wish to run the scripts yourself, there are several preparatory steps that are required:

1. Acquire the data. The data required to run the scripts have not been included in the repo, however, the data are available on request from Peter Kamerman ([email protected]⁠). Once the data have been obtained, the files should be uploaded to the RStudio Server instance.

2. Clean the /outputs directory by entering make clean in the Terminal tab in RStudio.

⁠Run the pain-threshold analysis scripts

To run all the scripts (including the data cleaning scripts), enter make all in the Terminal tab in RStudio.

⁠Shutting down

Once done, log out of RStudio Server and enter the following into a terminal to stop the Docker container: docker stop pangolin. If you then want to remove the container, enter: docker rm pangolin. If you also want to remove the Docker image you downloaded, enter: docker rmi kamermanpr/docker-pangolin-circadian:v1.0.0