Installation

Availability #

The OBITools are open source and protected by the CeCILL 2.1 license.

All the sources of the OBITools4 can be downloaded from the metabarcoding GitHub server ( https://github.com/metabarcoding).

Prerequisites #

The OBITools4 are developed using the GO programming language, we stick to the latest version of the language. If you want to download and compile the sources yourself, you first need to install the corresponding compiler on your system. 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.

Whichever installation you choose, you will need to ensure that a C compiler is available on your system.

Installation #

Using the installation script #

An installation script that compiles the new OBITools4 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:

curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash

By default, the script installs the OBITools4 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 previous OBITools . 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:

  • --install-dir|-i <PATH>: Directory where obitools are installed (as example use /usr/local not /usr/local/bin).

  • --obitools-prefix|-p: 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:

curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.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.