Supplementary Code for Publication

Overview over Software Environment

• This repository contains code to train SIAMCAT models with augmented samples
• The code is written in R and executed in a docker container (based on rocker/tidyverse)
• Caching and workflow is control using Drake and tidyverse
• gnu make is used to start the container
• Smaller models from the publication are shipped with this repository, but full models can be build from the supplied code

Installation

• this program only requires docker and gnu make on the system
  • in Ubuntu or similar, this can be done using sudo apt install make dockerd
  • this program was only tested on linux machines, but should run on any x86 or x64 system, but NOT M1 processors
• this process tested on SLES15 and Ubuntu 20.04
• Installation time depends on your internet connection
  • The size of the docker image is 2.15GB compressed (download size) and 6.15GB decompressed (final size on hard-drive)

Run

• start an r-studio server within this repository: make env
  • this command will download the docker image & start the container
  • it will also inform you about the url at which the container has been started (localhost:4444 or your system name like ubuntu:4444)
    • if the port 4444 is already in use, you need to change it to some other number within the Makefile
  • type the corresponding url into a web-browser
• The credentials are:
  • user : rstudio
  • password: tesseract
• you can send execute the scripts within src/ in order
  • src/00_main_build.R is the main entry point, including further comments on the individual scripts
  • it also contains a minimal example that will build models based on bacterial abundances as used in the manuscript
  • the resulting SIAMCAT models will be saved in rds format, which is a native data type for R data objects
• the example_output directory pre-computed results as a result of testing this repository

Stop

• once you are down, you can simply stop and/or remove the container
  • identify the ID container using docker ps (e.g. 09d17d227d)
  • docker rm -f ID