Genetic identification of the common bristlenose

Rupert A. Collins // August 2023

BACKGROUND

This README file describes the software requirements to run the ancistr analysis on an Ubuntu system. The R script scripts/ancistr.R searches the NCBI GenBank nucleotide database for Ancistrus sequence data (COI gene), and then runs a phylogenetic and sequence similarity analysis to estimate the closest relatives of the common bristlenose catfish Ancistrus sp. (3). The Quarto script ancistr.qmd executes this R script and generates an html output report ancistr.html (not committed to git).

INSTALLATION

Install prerequisites from Ubuntu repositories, and install Quarto:

sudo apt update
sudo apt install make build-essential libssl-dev zlib1g-dev libbz2-dev libreadline-dev libsqlite3-dev wget curl llvm libncursesw5-dev xz-utils tk-dev libxml2-dev libxmlsec1-dev libffi-dev liblzma-dev git mafft
# see more recent versions of quarto at https://github.com/quarto-dev/quarto-cli/releases/latest or https://quarto.org/docs/get-started/
wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.3.450/quarto-1.3.450-linux-amd64.deb
sudo apt install ./quarto-1.3.450-linux-amd64.deb

Install R (may take up to ten minutes):

# clone R installer
git clone https://github.com/jcrodriguez1989/renv-installer.git ~/.renv
# define environment variable RENV_ROOT
echo 'export RENV_ROOT="$HOME/.renv"' >> ~/.bashrc
echo 'export PATH="$RENV_ROOT/bin:$PATH"' >> ~/.bashrc
# add renv init to your shell
echo -e 'if command -v renv 1>/dev/null 2>&1; then\n  eval "$(renv init -)"\nfi' >> ~/.bashrc
# restart shell
exec "$SHELL"
# install R v4.3.1
renv install 4.3.1

Clone this repository and install R packages (may take up to one hour):

# clone project repository
git clone https://github.com/boopsboops/ancistr.git
cd ancistr
# install R packages
Rscript -e "renv::restore()"

USAGE

Run the analysis and generate the report (may take up to five minutes):

# creates file 'ancistr.html'
# previous analyses are kept in dated folders in 'results/'
quarto render ancistr.qmd

CONTENTS (A-Z)

• assets/ - Required files.
  • ancistrus-coi.csv - comma delimited table of in-house COI sequence data
  • Ancistrus_sp(3).jpg - photo of the bristlenose catfish
• renv/ - Settings for the R environment.
• results/ - Storage directory of previous analyses. Ignored by git.
• scripts/ - R scripts.
  • ancistr.R - script to run the GenBank search and phylogenetic analysis
  • load-libs-funs.R - script loading up libraries and custom functions
• ancistr.qmd - quarto file to compile report and render as html
• ancistr.html - report output html file (ignored by git)
• LICENSE - Legal stuff
• README.md - This file
• renv.lock - R packages required and managed by renv
• .gitignore - files and directories ignored by git
• .Rprofile - activates renv
• .R-version - required version of R (used by renv-installer)