mirror of
https://github.com/metabarcoding/obitools4.git
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19 lines
2.9 KiB
JSON
19 lines
2.9 KiB
JSON
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"markdown": "# Installation of the *OBITools*\n\n## Availability of the *OBITools*\n\nThe *OBITools* are open source and protected by the [CeCILL 2.1 license](http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html).\n\nAll the sources of the [*OBITools4*](http://metabarcoding.org/obitools4) can be downloaded from the metabarcoding git server (https://git.metabarcoding.org).\n\n## Prerequisites\n\nThe *OBITools4* are developped using the [GO programming language](https://go.dev/), we stick to the latest version of the language, today the $1.21.4$. 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.\n\nWhatever the installation you decide for, you will have to ensure that a C compiler is available on your system.\n\n## Installation with the install script\n\nAn installation script that compiles the new *OBITools* on your Unix-like system is available online.\nThe easiest way to run it is to copy and paste the following command into your terminal\n\n::: {.cell execution_count=1}\n``` {.bash .cell-code}\ncurl -L https://metabarcoding.org/obitools4/install.sh | bash\n```\n:::\n\n\nBy default, the script installs the *OBITools* commands and other associated files into the `/usr/local` directory.\nThe names of the commands in the new *OBITools4* are mostly identical to those in *OBITools2*.\nTherefore, installing the new *OBITools* may hide or delete the old ones. If you want both versions to be \navailable on your system, the installation script offers two options:\n\n\n> -i, --install-dir Directory where *OBITools* are installed \n> (as example use `/usr/local` not `/usr/local/bin`).\n> \n> -p, --obitools-prefix Prefix added to the *OBITools* command names if you\n> want to have several versions of obitools at the\n> same time on your system (as example `-p g` will produce \n> `gobigrep` command instead of `obigrep`).\n\nYou can use these options by following the installation command:\n\n::: {.cell execution_count=2}\n``` {.bash .cell-code}\ncurl -L https://metabarcoding.org/obitools4/install.sh | \\\n bash -s -- --install-dir test_install --obitools-prefix k\n```\n:::\n\n\nIn 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`.\n\n\n## Compilation from sources\n\n",
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