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supersmartR Workshop

These resources were originally put together for a one-day workshop for the Gothenburg Global Biodiversity Centre, Gothenburg, Sweden on the 17th Sept. 2019.

To learn the supersmartR approach yourself, you can follow the instructions layed out in the slides.

supersmartR is a series of R packages that form a phylogenetic pipeline.

In this workshop we will introduce you to the packages, outline the steps of a simple phylogenetic pipeline and demonstrate the next steps for advancing and scaling up the method.

Base pipeline

Learning outcomes

  • Gain experience in the four existing supersmartR packages: phylotaR, restez, outsider, gaius.
  • Run simple phylogenetic pipeline
  • Develop own more complex pipeline
  • Develop R programming skills
  • Become aware of the different phylogenetic and computing options

Prerequisites

  • Computer
    • Operating system: Windows 10, Linux, OSX
    • 20 - 50 GB spare capacity
  • Software
  • Basic knowledge
    • R
    • Phylogenetics

(If you have a Windows computer, consider setting up dual-boot.)

R packages

Install dependant packages.

# remotes allows installation via GitHub
# install.packages(“remotes”)

library(remotes)
# install latest outsider
install_github("antonellilab/outsider.base")
install_github("antonellilab/outsider")
# install latest restez
install_github("hannesmuehleisen/MonetDBLite-R")
install_github("ropensci/restez")
# install latest phylotaR
install_github("ropensci/phylotaR")
# install latest gaius
install_github("antonellilab/gaius")

If you're computer is set-up correctly with the R packages and Docker, you should be able to run the below script without errors.

library(outsider)
repo <- "dombennett/om..hello.world"
module_install(repo = repo, force = TRUE)
hello_world <- module_import(fname = "hello_world", repo = repo)
hello_world()

Slides

Available online via assets/slides.pdf or Download

Data

Pre-compiled restez databases for the "2_large" and "3_supertree" pipelines. (These files will only be available on the day of the workshop.)

GenBank section Size (Gb) Link
Invertebrates 1.6 Download
Other mammals 0.1 Download
Other vertebrates 0.5 Download
Plants, fungi, algae 1.2 Download
Primates 0.3 Download
Rodents 0.1 Download

Also ...

Completed first step of "3_supertree" pipeline for Hystricomorpha: Download

Note: All files are ZIP compressed folders.


Details

Workshop teachers

Workshop sponsors

Gothenburg Global Biodiversity Centre
Nordic E-Infrastructure Collaboration
Swedish Life Watch

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