Using apt-get

Installing requirements using apt-get

Live notebook

If you prefer to see code in action, the full installation process with apt-get is available as a Notebook in Google Colab.

Packages

Run:

sudo apt-get update
sudo apt-get install \
  ruby ruby-sqlite3 r-base sqlite3 python3-pip \
  libcurl4-openssl-dev zlib1g zlib1g-dev \
  ncbi-blast+ hmmer bedtools idba prodigal mcl barrnap \
  diamond-aligner trnascan-se fastp fastani seqtk

Additional Software

Some of the software required by MiGA is not available in aptitude, but you can install it in your 64bit Linux machine using:

## FaQCs
wget -O FaQCs \
  "https://github.com/LANL-Bioinformatics/FaQCs/releases/download/2.10/FaQCs_linux_x86_64"
sudo install FaQCs /usr/bin/ && rm FaQCs

## Falco
wget -O falco.tar.gz \
  "https://github.com/smithlabcode/falco/releases/download/v1.2.1/falco-1.2.1.tar.gz"
tar zxf falco.tar.gz
( cd falco-1.2.1 \
    && ./configure CXXFLAGS="-O3 -Wall" \
    && make && sudo make install
) > /dev/null
rm -rf falco-1.2.1 falco.tar.gz

JAVA VM

If you want support for RDP classifications, you'll need any working Java VM. For example, you could install Temurin as follows:

wget -O - https://packages.adoptium.net/artifactory/api/gpg/key/public \
  | sudo apt-key add -
echo "deb https://packages.adoptium.net/artifactory/deb \
  $(awk -F= '/^VERSION_CODENAME/{print$2}' /etc/os-release) main" \
  | sudo tee /etc/apt/sources.list.d/adoptium.list
sudo apt-get update
sudo apt-get install temurin-21-jdk

MyTaxa utils

If you want to activate the MyTaxa and MyTaxa Scan steps, follow the instructions to install the MyTaxa Utils.