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

If you have apt-get, execute:

sudo apt-get update
sudo apt-get install \
ruby ruby-sqlite3 r-base sqlite3 python \
libcurl4-openssl-dev zlib1g zlib1g-dev \
ncbi-blast+ hmmer bedtools idba prodigal \
mcl barrnap diamond-aligner
sudo ln -s $(which diamond-aligner)

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
curl -Lso FaQCs \
"https://github.com/LANL-Bioinformatics/FaQCs/releases/download/2.10/FaQCs_linux_x86_64"
sudo install FaQCs /usr/bin/ && rm FaQCs
## Falco
curl -Lso falco.tar.gz \
"https://github.com/smithlabcode/falco/releases/download/v0.2.4/falco-0.2.4.tar.gz"
tar zxf falco.tar.gz
( cd falco-0.2.4 \
&& ./configure CXXFLAGS="-O3 -Wall" \
&& make && sudo make install
) > /dev/null
rm -rf falco-0.2.4
## Fastp
curl -Lso fastp "http://opengene.org/fastp/fastp"
sudo install fastp /usr/bin/ && rm fastp
# FastANI
curl -Lso fastani-Linux64-v1.32.zip \
"https://github.com/ParBLiSS/FastANI/releases/download/v1.32/fastani-Linux64-v1.32.zip"
unzip fastani-Linux64-v1.32.zip fastANI > /dev/null && rm fastani-Linux64-v1.32.zip
sudo install fastANI /usr/bin/ && rm fastANI

MyTaxa utils

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