QIIME2

QIIME2 is a compilation of bioinformatic Python based softwares that works on a conda enviroment. For this reason, it is necessary to install Miniconda to provide this package manager and conda enviroment. Once Miniconda is successfully installed, QIIME2 requires a new enviroment for its own functioning. You can follow the installing QIIME2 official guide for more information.

It should be emphasised that QIIME2 conda enviroment must be activated before running the importQC, OTU_classifier, OTU_decontam and diversity scripts, as they use qiime commands implemented in this enviroment.

1. Download enviroment file and enviroment creation (check the latest QIIME2 package in this link):

wget https://data.qiime2.org/distro/core/qiime2-2023.7-py38-linux-conda.yml
conda env create -n qiime2 --file qiime2-2023.7-py38-linux-conda.yml

For activating this enviroment use:

conda activate qiime2

R packages

As this code depends on other R packages, installation process can be quite long and devtools and BiocManager packages are required for other packages installation.

Sys.setenv("R_REMOTES_NO_ERRORS_FROM_WARNINGS"=TRUE)

if (!requireNamespace(c("BiocManager", "devtools"), quietly = TRUE))
    install.packages(c("BiocManager", "devtools"))


# Install devtools packages
pkg <- c("cafferychen777/ggpicrust2", "pmartinezarbizu/pairwiseAdonis/pairwiseAdonis")
devtools::install_github(pkg)

# Install BiocManager packages
pkg <- c("lefser", "decontam")
BiocManager::install(pkg)

# Install CRAN packages
pkg <- c("ggplot2", "dplyr", "ape", "glue", "tidyr", "reshape2", "stringr", "tibble", "readr", "tidyverse", "ggprism" , "patchwork", "MicrobiomeStat", "Maaslin2", "ggh4x", "GGally")
install.packages(pkg)

In this case, before running alpha_plot, beta_plot and lefse R scripts, conda qiime2 enviroment has to be deactivated (you must be in the base enviroment) with the following command:

conda deactivate

PICRUSt2

Similar to QIIME2 software, PICRUSt2 program requires a conda enviroment creation to run this software functions. PICRUSt2 installation process is fully explained in the PICRUSt2 official installation gide. We recommend from source installation to make this process easier, following the next steps:

1. Download the latest package release (available in this link):

wget https://github.com/picrust/picrust2/archive/v2.5.2.tar.gz
tar xvzf  v2.5.2.tar.gz
cd picrust2-2.5.2/

2. Creating and activating PICRUSt2 enviroment:

conda env create -f picrust2-env.yaml
conda activate picrust2
pip install --editable .

3. Verifying installation:

pytest