obitools4/doc/book/installation.qmd

# Installation of the *OBITools*

## Availability of the *OBITools*

The *OBITools* are open source and protected by the [CeCILL 2.1 license](http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html).

All the sources of the [*OBITools4*](http://metabarcoding.org/obitools4) can be downloaded from the metabarcoding git server (https://git.metabarcoding.org).

## Prerequisites

The *OBITools4* are developped using the [GO programming language](https://go.dev/), we stick to the latest version of the language, today the $1.27$. If you want to download and compile the sources yourself, you first need to install the corresponding compiler on your system. Some computations (distances between k-mers) use the experimental `simd` package of Go: the `Makefile` compiles them with `GOEXPERIMENT=simd`, and the installation script uses a Go 1.27 compiler for that reason. The resulting programs run on any processor, a portable code being used when no SIMD instruction is available. Some parts of the soft are also written in C, therefore a recent C compiler is also requested, GCC on Linux or Windows, the Developer Tools on Mac.

Whatever the installation you decide for, you will have to ensure that a C compiler is available on your system.

## Installation with the install script

An installation script that compiles the new *OBITools* on your Unix-like system is available online.
The easiest way to run it is to copy and paste the following command into your terminal

```{bash}
#| eval: false
curl -L https://metabarcoding.org/obitools4/install.sh | bash
```

By default, the script installs the *OBITools* commands and other associated files into the `/usr/local` directory.
The names of the commands in the new *OBITools4* are mostly identical to those in *OBITools2*.
Therefore, installing the new *OBITools* may hide or delete the old ones. If you want both versions to be 
available on your system, the installation script offers two options:


>  -i, --install-dir       Directory where *OBITools* are installed 
>                          (as example use `/usr/local` not `/usr/local/bin`).
> 
>  -p, --obitools-prefix   Prefix added to the *OBITools* command names if you
>                          want to have several versions of obitools at the
>                          same time on your system (as example `-p g` will produce 
>                          `gobigrep` command instead of `obigrep`).

You can use these options by following the installation command:

```{bash}
#| eval: false
curl -L https://metabarcoding.org/obitools4/install.sh | \
      bash -s -- --install-dir test_install --obitools-prefix k
```

In this case, the binaries will be installed in the `test_install` directory and all command names will be prefixed with the letter `k`. Thus `obigrep` will be named `kobigrep`.


## Compilation from sources