mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-11-09 17:24:41 +00:00
Eric Coissac
db2b398dd0
This commit updates the project to use Go version 1.27 for all build and testing processes. It also introduces support for experimental SIMD code compilation, enabling it by default while ensuring a portable scalar fallback is available. Documentation has been updated to reflect the new Go version and the use of the experimental SIMD package.
52 lines
2.8 KiB
Plaintext
52 lines
2.8 KiB
Plaintext
# Installation of the *OBITools*
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## Availability of the *OBITools*
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The *OBITools* are open source and protected by the [CeCILL 2.1 license](http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html).
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All the sources of the [*OBITools4*](http://metabarcoding.org/obitools4) can be downloaded from the metabarcoding git server (https://git.metabarcoding.org).
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## Prerequisites
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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.
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Whatever the installation you decide for, you will have to ensure that a C compiler is available on your system.
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## Installation with the install script
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An installation script that compiles the new *OBITools* on your Unix-like system is available online.
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The easiest way to run it is to copy and paste the following command into your terminal
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```{bash}
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#| eval: false
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curl -L https://metabarcoding.org/obitools4/install.sh | bash
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```
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By default, the script installs the *OBITools* commands and other associated files into the `/usr/local` directory.
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The names of the commands in the new *OBITools4* are mostly identical to those in *OBITools2*.
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Therefore, installing the new *OBITools* may hide or delete the old ones. If you want both versions to be
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available on your system, the installation script offers two options:
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> -i, --install-dir Directory where *OBITools* are installed
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> (as example use `/usr/local` not `/usr/local/bin`).
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>
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> -p, --obitools-prefix Prefix added to the *OBITools* command names if you
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> want to have several versions of obitools at the
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> same time on your system (as example `-p g` will produce
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> `gobigrep` command instead of `obigrep`).
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You can use these options by following the installation command:
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```{bash}
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#| eval: false
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curl -L https://metabarcoding.org/obitools4/install.sh | \
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bash -s -- --install-dir test_install --obitools-prefix k
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```
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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`.
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## Compilation from sources
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