1. Requirements and Installation
Complete instructions for installing paprica on OSX can be found here. Linux users should have little difficulty following those instructions with some common-sense modifications. There is also a linux_install.sh script in the repository that will, in theory, install paprica and all its dependencies. However, I recommend that you use this script as a guide and not simply execute it.
Paprica requires a bash equipped, Linux-like operating environment with at least 8 Gb RAM. It was developed on Ubuntu. I do not regularly test it on OSX, but I hear that it works fine. Paprica will also work in Windows 10 via the Windows Subsystem for Linux and is regularly tested in that environment.
The paprica-run.sh script relies on several open-source tools to function. All of these tools are mainstream and useful on their own if you’re working with 16S rRNA gene data. Required tools for paprica-run.sh that should be located in your path are:
- Python 3.6 or higher, callable as Python3
- The following Python modules: pandas, joblib, Biopython, numpy, termcolor
- Infernal, (including the easel/miniapps subdirectory*)
- gappa
- Seqmagik
- epa-ng
In addition this software is recommended for viewing the trees produced by pplacer:
Archaeopteryx (optional but highly recommended, it will allow you to view the phyloxml “fat” trees produced by gappa in the paprica-place_it.py script).
If you want to build the database from scratch you need all of the dependencies for paprica-run.sh plus:
- RAxML (paprica will assume the combiled binary is standard-RAxML/raxmlHPC-PTHREADS-AVX2)
- RAxML-ng (yes, right now you need both RAxML-ng and RAxML, we're working in it...)
- Pathway-Tools
- The Python module ete3
Last, if you use the paprica-mg.py or paprica-mt.py extensions for metagenomic or metatranscriptomic analysis you will need:
- DIAMOND
- BWA
*Easel is included as part of the Infernal package. You simply need to make sure that infernal/easel/miniapps is included in your path. For OSX users easel might be in a slightly different location, refer to this tutorial.