/bistorta_vivipara_translocation

Bioinformatics pipeline for "Experimental evidence on the influence of root-associated fungi on plant growth along altitude"

Primary LanguageR

Bioinformatics pipeline for "Experimental evidence on the influence of root-associated fungi on plant growth along altitude"

This pipeline is a pre-release version of the OptimOTU pipeline, which is implemented in R using the {targets} pipeline tool. It is probably difficult to run it outside of the CSC Puhti computing cluster where it was developed and executed for this project, and the code is included primarily for reference purposes to accompany the paper. A more portable and user-friendly execution process will be implemented in the public release of the OptimOTU pipeline R package.

That said, in principle the steps to execute it would be:

  1. Clone this Git repository

  2. Install all prerequisites listed in conda/bistorta_vivipara_pipeline.yaml, either using conda or by other means. If using conda, activate the conda environment.

  3. Download ProtaxFungi (link TBD) and unzip it into the sister directory

  4. Download the raw sequence files (link TBD) into sequences/01_raw

  5. In R:

library(targets)
tar_make()