# 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](https://colab.research.google.com/gist/lmrodriguezr/78f2f48eadce96bc2dd526fd194fb00a).

### Packages

Run:

```bash
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 spades prodigal mcl barrnap diamond-aligner \
  fastp fastani trnascan-se 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:

```bash
## FaQCs
wget -O FaQCs \
  "https://github.com/LANL-Bioinformatics/FaQCs/releases/download/2.12/FaQCs_linux_x86_64"
sudo install FaQCs /usr/bin/ && rm FaQCs

## Falco
wget -O falco.tar.gz \
  "https://github.com/smithlabcode/falco/releases/download/v1.2.5/falco-1.2.5.tar.gz"
tar zxf falco.tar.gz
( cd falco-1.2.5 \
    && ./configure CXXFLAGS="-O3 -Wall" \
    && make && sudo make install
)
rm -rf falco-1.2.5 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:

```bash
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](https://github.com/bio-miga/miga/blob/main/manual/part2/part5/workflow.md#mytaxa) and [MyTaxa Scan](https://github.com/bio-miga/miga/blob/main/manual/part2/part5/workflow.md#mytaxa-scan) steps, follow the instructions to install the [MyTaxa Utils](https://manual.microbial-genomes.org/part2/requirements/mytaxa).