Testing the setup

If you would like to test the installation of the ARMOR workflow, the repository contains a small example data set. This data set contains paired compressed FASTQ files for four samples from the GSE52778 data set, containing only reads aligning to the first 10M bases of chromosome 1 (in the FASTQ directory). In addition, the directory contains a metadata table with information about the four samples, and a reference directory with two collections of reference files (Gencode v28 and Ensembl v93). The provided config.yaml file is already set up for the example data set and will use conda environments to manage the required software and R.

The expression to create the design matrix (via design) and the contrast matrix (via contrast) is specified in the config.yaml file. More details about how to create design matrix and contrast matrix are in stats::model.matrix and limma::makeContrasts. The data in metadata.txt is used to create the design and contrast matrix. You can view the design and contrast matrix with

snakemake --use-conda checkinputs

You can test your conda and R configuration immediately by running the workflow on the example data with

snakemake --use-conda.

If you have all the software in your path or you want to use a manually created conda environment + system R installation, run the workflow with

snakemake.

See https://github.com/csoneson/ARMOR/wiki/Managing-software for an explanation of the three different ways to manage the software.