This is a graph of the ARMOR (Automated Reproducible MOdular RNA-seq) workflow. It shows all the steps in the workflow: Blue circles are rules run in
R, orange circles from software called as shell commands. Dashed lines and light-colored circles are optional rules, controlled in
Assuming that snakemake and conda are installed (see above), here is how to quickly get started. Simply download and run ARMOR on the example dataset with following commands:
git clone https://github.com/csoneson/ARMOR.git cd ARMOR && snakemake --use-conda
This will clone the ARMOR repository to your computer, create conda environments with the required software and R packages installed and run the workflow on the small example dataset that we provide.
Note: The installation of the required software in the conda environments will take some time! And, this will likely not work on Mac OS X unless your system is setup with the necessary libraries to compile R packages; see Managing software
Using the ARMOR workflow
To use the ARMOR workflow on your own data, follow the steps outlined below carefully.
Clone this repository to your local machine and set the working directory to the cloned repository:
git clone https://github.com/csoneson/ARMOR.git cd ARMOR
Make sure that all the necessary software is available. This can be done in three ways:
Testing the setup
We provide a small example data set that you can use to test your setup: See Testing the setup.
Example of a real data analysis
If you want to see a real data analysis with the ARMOR workflow, please have a look at the
chiron_readataworkflow branch of the ARMOR GitHub repository. You can find it here. This example uses conda to manage the required software, including R and the installation of all R packages. More details can be found in the "Real data walk-through" section of our preprint:
S Orjuela*, R Huang*, KM Hembach*, MD Robinson, C Soneson: ARMOR: an Automated Reproducible MOdular workflow for preprocessing and differential analysis of RNA-seq data. bioRxiv doi: https://doi.org/10.1101/575951