If you prefer to see code in action, the full installation process with apt-get is available as a .
sudo apt-get update
sudo apt-get install \
ruby ruby-sqlite3 r-base sqlite3 libcurl4-openssl-dev zlib1g zlib1g-dev pigz \
ncbi-blast+ hmmer bedtools idba prodigal mcl barrnap diamond-aligner \
fastp fastani trnascan-se seqtk
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/v1.2.3/falco-1.2.3.tar.gz"
tar zxf falco.tar.gz
( cd falco-1.2.3 \
&& ./configure CXXFLAGS="-O3 -Wall" \
&& make && sudo make install
)
rm -rf falco-1.2.3 falco.tar.gz
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
