Install software and packages
To get started quickly during the course, we ask you to prepare a few things before the start of the course.
We will use the following software:
Please install these following the instructions below.
Install four tools using Miniconda
Conda is a package management system and environment management system that allow to quickly install, run and update packages and their dependencies. The first four tools can be easily installed using conda, we suggest to use Miniconda. To install miniconda, follow the instructions for MacOS, Windows or Linux.
After installing miniconda, create a file named NCCR_p3.yaml
with:
name: NCCR_p3
channels:
- conda-forge
- defaults
- bioconda
dependencies:
- python=3.8
- fastqc=0.11.9
- motus=3.0.1
- trimmomatic=0.39
- mapseq=1.2.6
In the terminal you can then type:
conda env create -f NCCR_p3.yaml
To create an environment with the four tools that we will run in the terminal. You need to activate the environment before using it:
source activate NCCR_p3
Note that mOTUs require around 7Gb of space and it will download 3.5 Gb when installing. Hence the installation can take a few minutes.
Problems installing with conda
If you have problem installing the conda environment, it might be due to the size required for mOTUs. We suggest to remove motus and install it with pip
. First create a new yaml file (names NCCR_p3_test2.yaml
):
name: NCCR_p3_test2
channels:
- conda-forge
- defaults
- bioconda
dependencies:
- python=3.8
- fastqc=0.11.9
- bwa
- samtools
- pip
- trimmomatic=0.39
- mapseq=1.2.6
Create and activate the environment:
conda env create -f NCCR_p3_test2.yaml
source activate NCCR_p3_test2
Install mOTUs with pip:
pip install motu-profiler
And download the database manually:
motus downloadDB
Installing R packages
Within R (we suggest to use R studio), type:
##R Version 4.0.2 or above
#tidyverse packages for plotting and data wrangling
install.packages("tidyverse")
#SIAMCAT
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SIAMCAT")