Installation and Prerequisites

Prerequisites

This program is intended to be used under Linux systems. The program itself is a bash script, which invokes several Python and R scripts. In the terminal, the following commands should be recognisable:

awk (v. 5.1.0)
sed (v. 4.8)
parallel (v. 20200322)
python (v. 3.8.6)
Rscript (v. 4.0.3)

The versions of the mentioned above programs are those with which the rRNADif was tested. The script itself also depends on several python (pandas v 1.1.0, biopython v 1.7.8) and R (ape v 5.4-1, dplyr 1.0.2, tidyr v. 1.1.2, ggplot2 v 3.3.2) libraries.

Also, rRNADif depends on barrnap, mafft and fasttree software, which could be installed via conda.

Installation

Detailed walkthrough

The rRNADif is a bash script, which connects several R and python scripts. Therefore it is ready to be used as soon as prerequisites are satisfied. 0. To install Anaconda or Miniconda please refer to the official instructions.

  1. To install awk, sed, parallel, python (python3) and Ruse package manager for your Linux distribution. It can be apt install for Ubuntu, yum install for Fedora and pacman -S for Arch. Or you can run conda install parallel python r-base, if you have Anaconda or Miniconda installation.
  2. To install python libraries you can run pip install pandas biopython (or via conda install pandas biopython)
  3. To install R libraries you can run in terminal install.packages(c("ape", "dplyr", "tidyr", "ggplot2"))(or via conda install r-ape r-dplyr r-tidyr r-ggplot2)
  4. To install barrnap, mafft and fasttree you should run conda install barrnap mafft fasttree
  5. (optional) To install other software (for MSA or phylogeny) you can run conda install <name-of-the-package>, if it is available in anaconda or bioconda repositories. Options within rRNADif are available there, so the install should take only one command (ex. conda install muscle clustalw iqtree raxml)
note

rrnadif.sh is intended to be run from the script location directory. You can edit ~/.bashrc profile to invoke it from everywhere in your system.

warning

Before you begin to use rRNADif please read Get started guide

Conda easy install

  1. Install Miniconda
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh

Then restart the terminal or run source ~/.bashrc

  1. Configure channels
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
  1. Install software
conda create -n rrnadif python=3.8 biopython pandas parallel r-base r-ape r-dplyr r-tidyr r-ggplot2 barrnap mafft fasttree
  1. Activate an environment and run rRNADif under it
conda activate rrnadif
cd rRNADif # go to the repo location
sh rrnadif.sh -h
warning

Before you begin to use rRNADif please read Get started guide

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