edna-dada2

Maine eDNA

Divisive Amplicon Denoising Algorithm dada2

charlie wiki

Requirements

• Install into your home R library 2 packages from github

  • compressr

  • dadautils

• Load the dada2 module

module use /mod/bigelow
module load dada2

Organization

• config configuration files in yaml format

• docs miscellaneous notes

• pbs shell scripts to use when calling qsub

• rscript R scripts to manage workflows

• scratch a place to put files that will be ignored by git

Workflows

Whether as a PBS job, cron or manually workflow scripts accept at least one argument (configuration filename)

$ Rscript /path/to/Rscript/my_script.R /path/to/config/file.yaml

The config file will contain among other things the identities of input and output paths. The output path will be populated with subdirectories and a diagnostic and results files. Diagnostic files may include software audits and output logs. Results files will vary by script.

Configuration file

A configuration file is a text file that is specially formatted to be machine readable. While there are a variety of formats to chose among, we have chosen yaml as our preferred format.
See the wiki page for details.