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
supersmartRapproach 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.
- Gain experience in the four existing
supersmartRpackages: 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
- Computer
- Operating system: Windows 10, Linux, OSX
- 20 - 50 GB spare capacity
- Software
- R (> 3.5)
- RStudio
- Desktop Docker (Linux containers)
- Basic knowledge
- R
- Phylogenetics
(If you have a Windows computer, consider setting up dual-boot.)
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()
Available online via assets/slides.pdf or
Download
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.
| Gothenburg Global Biodiversity Centre |  |
| Nordic E-Infrastructure Collaboration |
| Swedish Life Watch |  |