curl -L https://metabarcoding.org/obitools4/install.sh | bash1 Installation of the OBITools
1.1 Availability of the OBITools
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 git server (https://git.metabarcoding.org).
1.2 Prerequisites
The OBITools4 are developped using the GO programming language, we stick to the latest version of the language, today the . 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.
Whatever the installation you decide for, you will have to ensure that a C compiler is available on your system.
1.3 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
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/localnot/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 gwill producegobigrepcommand instead ofobigrep).
You can use these options by following the installation command:
curl -L https://metabarcoding.org/obitools4/install.sh | \
bash -s -- --install-dir test_install --obitools-prefix kIn 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.