> For the complete documentation index, see [llms.txt](https://manual.microbial-genomes.org/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://manual.microbial-genomes.org/master/part2/requirements/apt-get.md).

# 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 Collab](https://colab.research.google.com/drive/1xP5l0p1osRwrzw39IyAplRhbVeCdgmsJ).

## Essentials

If you have `apt-get`, execute:

```bash
# General-purpose software
sudo apt-get update
sudo apt-get install ruby ruby-sqlite3 r-base sqlite3 python \
  libcurl4-openssl-dev openjdk-8-jdk
# Bioinformatics software
sudo apt-get install ncbi-blast+ hmmer bedtools idba \
  prodigal mcl barrnap scythe fastqc diamond-aligner
sudo ln -s $(which diamond-aligner) /usr/bin/diamond
```

## IDBA

The index of some distros may still have an old version of IDBA that didn't build the IDBA-UD flavor (you'll need at least v1.1.3-2). Check first if you have it:

```bash
idba_ud
```

If you don't, you can get it by adding the Ubuntu Universe source to APT:

```bash
echo 'deb http://us.archive.ubuntu.com/ubuntu/ cosmic universe' \
  | sudo tee /etc/apt/sources.list.d/ubuntu-universe.list
sudo apt-get update
sudo apt-get install idba
```

Or install it directly from the DEB package:

```bash
wget http://ftp.br.debian.org/debian/pool/main/i/idba/idba_1.1.3-3_amd64.deb
sudo apt-get install ./idba_1.1.3-3_amd64.deb
```

## SolexaQA++

Next, you'll need to install SolexaQA++. If you have a 64-bits Linux:

```bash
curl -L -o SolexaQA++_v3.1.7.1.zip \
  "https://downloads.sourceforge.net/project/solexaqa/src/SolexaQA%2B%2B_v3.1.7.1.zip"
unzip -p SolexaQA++_v3.1.7.1.zip Linux_x64/SolexaQA++ > SolexaQA++
sudo install SolexaQA++ /usr/bin/
```

If you have 32-bits Linux, you can build SolexaQA++ from source:

```bash
sudo apt-get install libboost-dev libboost-filesystem-dev \
      libboost-regex-dev libboost-iostreams-dev
curl -L -o SolexaQA++_v3.1.7.1.zip \
  "https://downloads.sourceforge.net/project/solexaqa/src/SolexaQA%2B%2B_v3.1.7.1.zip"
unzip SolexaQA++_v3.1.7.1.zip 'source/*'
cd source && make
sudo install source/SolexaQA++ /usr/bin/
```

## FastANI

FastANI is optional, but it may be required to search certain databases. It can be used instead of BLAST ANI to speed up indexing. If you have a 64-bits Linux:

```bash
curl -L -o fastani-Linux64-v1.3.zip \
  "https://github.com/ParBLiSS/FastANI/releases/download/v1.3/fastani-Linux64-v1.3.zip"
unzip fastani-Linux64-v1.3.zip fastANI
sudo install fastANI /usr/bin/
```

If you have a 32-bits Linux, you can build it from source following the [FastANI installation](https://github.com/ParBLiSS/FastANI/blob/master/INSTALL.txt).

## R packages

The full list of R packages is automatically installed by MiGA. However, we will install one package here to make sure everything is properly initialized.

```bash
Rscript -e "install.packages('ape', repos = 'http://cran.rstudio.com/')"
```

## MyTaxa utils

If you want to activate the [MyTaxa](https://github.com/bio-miga/miga/tree/2987d0a747581e7e0515fac7bf98f7935fe4b24b/manual/part2/part5/workflow.md#mytaxa) and [MyTaxa Scan](https://github.com/bio-miga/miga/tree/2987d0a747581e7e0515fac7bf98f7935fe4b24b/manual/part2/part5/workflow.md#mytaxa-scan) steps, follow the instructions to install the [MyTaxa Utils](/master/part2/requirements/mytaxa.md).


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