1639 lines
26 KiB
HTML
1639 lines
26 KiB
HTML
<!DOCTYPE html>
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<html lang="en-us" dir="ltr">
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<head>
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<meta charset="UTF-8">
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<meta name="description" content="
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Availability
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#
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The OBITools are open source and protected by the
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CeCILL 2.1 license.
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All the sources of the
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OBITools4
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can be downloaded from the metabarcoding GitHub server (
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https://github.com/metabarcoding).
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Prerequisites
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#
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The
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OBITools4
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are developed using the
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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.">
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<meta name="theme-color" media="(prefers-color-scheme: light)" content="#ffffff">
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<meta name="theme-color" media="(prefers-color-scheme: dark)" content="#343a40">
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<meta name="color-scheme" content="light dark"><meta property="og:url" content="http://metabar:8888/obidoc/docs/installation/">
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<meta property="og:site_name" content="OBITools4 documentation">
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<meta property="og:title" content="Installation">
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<meta property="og:description" content="Availability # The OBITools are open source and protected by the CeCILL 2.1 license.
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All the sources of the OBITools4 can be downloaded from the metabarcoding GitHub server ( https://github.com/metabarcoding).
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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.">
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<meta property="og:locale" content="en_us">
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<meta property="og:type" content="website">
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<title>Installation | OBITools4 documentation</title>
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<link rel="alternate" type="application/rss+xml" href="http://metabar:8888/obidoc/docs/installation/index.xml" title="OBITools4 documentation" />
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<nav>
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<h2 class="book-brand">
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<a class="flex align-center" href="/obidoc/"><img src="/obidoc/obitools_logo.jpg" alt="Logo" class="book-icon" /><span>OBITools4 documentation</span>
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<span>Docs</span>
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<ul>
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<li>
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<a href="/obidoc/docs/about/" class="">About</a>
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<li>
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<a href="/obidoc/docs/installation/" class="active">Installation</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/docs/principles/" class="">General operating principles</a>
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<ul>
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</ul>
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<li>
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<input type="checkbox" id="section-08756b4c1f14be6ee584ece005b9f621" class="toggle" />
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<label for="section-08756b4c1f14be6ee584ece005b9f621" class="flex justify-between">
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<a role="button" class="">File formats</a>
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</label>
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<ul>
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<input type="checkbox" id="section-933c2e64b905b84e22aa5273cea2d0bd" class="toggle" />
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<label for="section-933c2e64b905b84e22aa5273cea2d0bd" class="flex justify-between">
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<a role="button" class="">Sequence file formats</a>
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</label>
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<ul>
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<li>
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<a href="/obidoc/formats/fasta/" class="">FASTA file format</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/formats/fastq/" class="">FASTQ file format</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/formats/genbank/" class="">GenBank Flat File format</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/formats/embl/" class="">EMBL Flat File format</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/docs/file_format/sequence_files/csv/" class="">CSV format</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/formats/json/" class="">JSON format</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/docs/file_format/sequence_files/annotations/" class="">Annotation of sequences</a>
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<ul>
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</ul>
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</li>
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</ul>
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<input type="checkbox" id="section-0258ae1c222f9a38cc1b75254c93b0f4" class="toggle" />
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<label for="section-0258ae1c222f9a38cc1b75254c93b0f4" class="flex justify-between">
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<a role="button" class="">Taxonomy file formats</a>
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</label>
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<ul>
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<li>
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<a href="/obidoc/docs/file_format/taxonomy_file/csv_taxdump/" class="">CSV formatted taxdump</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/docs/file_format/taxonomy_file/ncbi_taxdump/" class="">NCBI taxdump</a>
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<ul>
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</ul>
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</li>
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</ul>
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<li>
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<a href="/obidoc/formats/csv/" class="">The CSV format</a>
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<ul>
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</ul>
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</li>
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</ul>
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<li>
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<input type="checkbox" id="section-70b1e6e5ec7f3ccab643155fa50659b6" class="toggle" />
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<label for="section-70b1e6e5ec7f3ccab643155fa50659b6" class="flex justify-between">
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<a role="button" class="">Patterns</a>
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</label>
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<ul>
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<li>
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<a href="/obidoc/docs/patterns/regular/" class="">Regular Expressions</a>
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<li>
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<a href="/obidoc/docs/patterns/dnagrep/" class="">DNA Patterns</a>
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</li>
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</ul>
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<input type="checkbox" id="section-8223f464911a1fe6c655972143684e93" class="toggle" />
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<label for="section-8223f464911a1fe6c655972143684e93" class="flex justify-between">
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<a role="button" class="">The OBITools4 commands</a>
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</label>
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<ul>
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<li>
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<a href="/obidoc/docs/commands/options/" class="">Shared command options</a>
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<ul>
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</ul>
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<input type="checkbox" id="section-8921ea65523c266b128dd4263232b0fc" class="toggle" />
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<label for="section-8921ea65523c266b128dd4263232b0fc" class="flex justify-between">
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<a role="button" class="">Basics</a>
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</label>
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<ul>
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<li>
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<a href="/obidoc/obitools/obiannotate/" class="">obiannotate</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/obitools/obicomplement/" class="">obicomplement</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obiconvert/" class="">obiconvert</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/obitools/obicount/" class="">obicount</a>
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<ul>
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</ul>
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</li>
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<a href="/obidoc/obitools/obicsv/" class="">obicsv</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obidemerge/" class="">obidemerge</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obidistribute/" class="">obidistribute</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obigrep/" class="">obigrep</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/obitools/obijoin/" class="">obijoin</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/obitools/obimatrix/" class="">obimatrix</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obisplit/" class="">obisplit</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/obitools/obisummary/" class="">obisummary</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obiuniq/" class="">obiuniq</a>
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<ul>
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</ul>
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</li>
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</ul>
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<li>
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<input type="checkbox" id="section-dbdf1bb5377572439394e60e08c30f50" class="toggle" />
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<label for="section-dbdf1bb5377572439394e60e08c30f50" class="flex justify-between">
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<a role="button" class="">Demultiplexing samples</a>
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</label>
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<ul>
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<li>
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<a href="/obidoc/obitools/obimultiplex/" class="">obimultiplex</a>
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<ul>
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</ul>
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<a href="/obidoc/obitools/obitagpcr/" class="">obitagpcr</a>
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<ul>
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</ul>
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</li>
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</ul>
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</li>
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<li>
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<input type="checkbox" id="section-aa98fedd067b51150db59691a8ea8edd" class="toggle" />
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<label for="section-aa98fedd067b51150db59691a8ea8edd" class="flex justify-between">
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<a role="button" class="">Sequence alignments</a>
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</label>
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<ul>
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<li>
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<a href="/obidoc/obitools/obiclean/" class="">obiclean</a>
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<ul>
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</ul>
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</li>
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<li>
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<input type="checkbox" id="section-7433746525d8c2b29b033f765c869acd" class="toggle" />
|
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<label for="section-7433746525d8c2b29b033f765c869acd" class="flex justify-between">
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<a href="/obidoc/obitools/obipairing/" class="">obipairing</a>
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</label>
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<ul>
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<li>
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<a href="/obidoc/docs/commands/alignments/obipairing/fasta-like/" class="">The FASTA-like alignment</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/docs/commands/alignments/obipairing/exact-alignment/" class="">Exact alignment</a>
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<ul>
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</ul>
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</li>
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</ul>
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</li>
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<li>
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<a href="/obidoc/obitools/obipcr/" class="">obipcr</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/obitools/obirefidx/" class="">obirefidx</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/obitools/obitag/" class="">obitag</a>
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<ul>
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</ul>
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</li>
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</ul>
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</li>
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<li>
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<input type="checkbox" id="section-5746f699d10490780dec8e30ab2dd3ce" class="toggle" />
|
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<label for="section-5746f699d10490780dec8e30ab2dd3ce" class="flex justify-between">
|
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<a role="button" class="">Taxonomy</a>
|
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</label>
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<ul>
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<li>
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<a href="/obidoc/obitools/obitaxonomy/" class="">obitaxonomy</a>
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<ul>
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</ul>
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</li>
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</ul>
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</li>
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<li>
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<input type="checkbox" id="section-3f50c4fe7ab436a56ae92897d5444956" class="toggle" />
|
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<label for="section-3f50c4fe7ab436a56ae92897d5444956" class="flex justify-between">
|
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<a role="button" class="">Advanced tools</a>
|
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</label>
|
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<ul>
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<li>
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<a href="/obidoc/obitools/obiscript/" class="">obiscript</a>
|
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<ul>
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</ul>
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</li>
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</ul>
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</li>
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<li>
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<input type="checkbox" id="section-549be3934679fcb82a232f6bd5435563" class="toggle" />
|
|
<label for="section-549be3934679fcb82a232f6bd5435563" class="flex justify-between">
|
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<a role="button" class="">Others</a>
|
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</label>
|
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<ul>
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<li>
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<a href="/obidoc/obitools/obimicrosat/" class="">obimicrosat</a>
|
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<ul>
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</ul>
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</li>
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</ul>
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</li>
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<li>
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<input type="checkbox" id="section-ceca4455173761e30cbc0a6dc2327167" class="toggle" />
|
|
<label for="section-ceca4455173761e30cbc0a6dc2327167" class="flex justify-between">
|
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<a role="button" class="">Experimentals</a>
|
|
</label>
|
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<ul>
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<li>
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<a href="/obidoc/obitools/obicleandb/" class="">obicleandb</a>
|
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/obitools/obiconsensus/" class="">obiconsensus</a>
|
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/obitools/obilandmark/" class="">obilandmark</a>
|
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<ul>
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</ul>
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</li>
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</ul>
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</li>
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<li>
|
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|
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<a href="/obidoc/docs/commands/tags/" class="">Glossary of tags</a>
|
|
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|
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</li>
|
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|
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</ul>
|
|
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</li>
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<li>
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<input type="checkbox" id="section-9b1bcd52530c59dc4819b1f61c128f54" class="toggle" />
|
|
<label for="section-9b1bcd52530c59dc4819b1f61c128f54" class="flex justify-between">
|
|
<a role="button" class="">Cookbook</a>
|
|
</label>
|
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<ul>
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<li>
|
|
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<a href="/obidoc/docs/cookbook/illumina/" class="">Analysing an Illumina data set</a>
|
|
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|
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<ul>
|
|
|
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</ul>
|
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</li>
|
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<li>
|
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<a href="/obidoc/docs/cookbook/ecoprimers/" class="">Designing new barcodes</a>
|
|
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<ul>
|
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</ul>
|
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</li>
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<li>
|
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<a href="/obidoc/docs/cookbook/local_genbank/" class="">Prepare a local copy of Genbank</a>
|
|
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|
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<ul>
|
|
|
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</ul>
|
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</li>
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<li>
|
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<a href="/obidoc/docs/cookbook/reference_db/" class="">Build a reference database</a>
|
|
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<ul>
|
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</ul>
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</li>
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<li>
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<a href="/obidoc/docs/cookbook/minion/" class="">Oxford Nanopore data analysis</a>
|
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<ul>
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</ul>
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</li>
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</ul>
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</li>
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<li>
|
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|
<span>Programming OBITools</span>
|
|
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<ul>
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<li>
|
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<a href="/obidoc/docs/programming/expression/" class="">Expression language</a>
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<ul>
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</ul>
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</li>
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<li>
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<input type="checkbox" id="section-6d580829a667b5cca790b286d99a10fe" class="toggle" />
|
|
<label for="section-6d580829a667b5cca790b286d99a10fe" class="flex justify-between">
|
|
<a href="/obidoc/docs/programming/lua/" class="">Lua: for scripting OBITools</a>
|
|
</label>
|
|
|
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|
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|
<ul>
|
|
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<li>
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<input type="checkbox" id="section-2fb081dac812d624eea5f4268fca9e26" class="toggle" />
|
|
<label for="section-2fb081dac812d624eea5f4268fca9e26" class="flex justify-between">
|
|
<a role="button" class="">Obitools Classes</a>
|
|
</label>
|
|
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<ul>
|
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<li>
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<a href="/obidoc/docs/programming/lua/obitools_classes/biosequence/" class="">BioSequence</a>
|
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<ul>
|
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|
</ul>
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</li>
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<li>
|
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|
<a href="/obidoc/docs/programming/lua/obitools_classes/biosequenceslice/" class="">BioSequenceSlice</a>
|
|
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<ul>
|
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</ul>
|
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</li>
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<li>
|
|
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|
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<a href="/obidoc/docs/programming/lua/obitools_classes/taxonomy/" class="">Taxonomy</a>
|
|
|
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|
<ul>
|
|
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</ul>
|
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</li>
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<li>
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<a href="/obidoc/docs/programming/lua/obitools_classes/taxon/" class="">Taxon</a>
|
|
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<ul>
|
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</ul>
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</li>
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<li>
|
|
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|
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<a href="/obidoc/docs/programming/lua/obitools_classes/mutex/" class="">Mutex</a>
|
|
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<ul>
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</ul>
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</li>
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</ul>
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</li>
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</ul>
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</li>
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</ul>
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</li>
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</ul>
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</li>
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</ul>
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</nav>
|
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<script>(function(){var e=document.querySelector("aside .book-menu-content");addEventListener("beforeunload",function(){localStorage.setItem("menu.scrollTop",e.scrollTop)}),e.scrollTop=localStorage.getItem("menu.scrollTop")})()</script>
|
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</div>
|
|
</aside>
|
|
|
|
<div class="book-page">
|
|
<header class="book-header">
|
|
|
|
<div class="flex align-center justify-between">
|
|
<label for="menu-control">
|
|
<img src="/obidoc/svg/menu.svg" class="book-icon" alt="Menu" />
|
|
</label>
|
|
|
|
<h3>Installation</h3>
|
|
|
|
<label for="toc-control">
|
|
|
|
<img src="/obidoc/svg/toc.svg" class="book-icon" alt="Table of Contents" />
|
|
|
|
</label>
|
|
</div>
|
|
|
|
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|
|
|
<aside class="hidden clearfix">
|
|
|
|
|
|
<nav id="TableOfContents">
|
|
<ul>
|
|
<li><a href="#availability">Availability</a>
|
|
<ul>
|
|
<li><a href="#prerequisites">Prerequisites</a></li>
|
|
</ul>
|
|
</li>
|
|
<li><a href="#installation">Installation</a>
|
|
<ul>
|
|
<li><a href="#using-the-installation-script">Using the installation script</a></li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</nav>
|
|
|
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|
|
</aside>
|
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|
|
</header>
|
|
|
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|
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|
|
<article class="markdown book-article"><h1 id="availability">
|
|
Availability
|
|
<a class="anchor" href="#availability">#</a>
|
|
</h1>
|
|
<p>The <em>OBITools</em> are open source and protected by the
|
|
<a href="http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html">CeCILL 2.1 license</a>.</p>
|
|
<p>All the sources of the
|
|
<a href="https://metabarcoding.org/obitools4"><abbr title="The fourth version of the OBITools, a set of unix command line tools for manipulating DNA metabarcoding data">OBITools4</abbr>
|
|
|
|
</a> can be downloaded from the metabarcoding GitHub server (
|
|
<a href="https://github.com/metabarcoding%29">https://github.com/metabarcoding)</a>.</p>
|
|
<h2 id="prerequisites">
|
|
Prerequisites
|
|
<a class="anchor" href="#prerequisites">#</a>
|
|
</h2>
|
|
<p>The
|
|
<a href="https://metabarcoding.org/obitools4"><abbr title="The fourth version of the OBITools, a set of unix command line tools for manipulating DNA metabarcoding data">OBITools4</abbr>
|
|
|
|
</a> are developed using the
|
|
<a href="https://go.dev/">GO programming language</a>, 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.</p>
|
|
<p>Whichever installation you choose, you will need to ensure that a C compiler is available on your system.</p>
|
|
<h1 id="installation">
|
|
Installation
|
|
<a class="anchor" href="#installation">#</a>
|
|
</h1>
|
|
<h2 id="using-the-installation-script">
|
|
Using the installation script
|
|
<a class="anchor" href="#using-the-installation-script">#</a>
|
|
</h2>
|
|
<p>An installation script that compiles the new
|
|
<a href="https://metabarcoding.org/obitools4"><abbr title="The fourth version of the OBITools, a set of unix command line tools for manipulating DNA metabarcoding data">OBITools4</abbr>
|
|
|
|
</a> 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:</p>
|
|
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-bash" data-lang="bash"><span style="display:flex;"><span>curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash
|
|
</span></span></code></pre></div><p>By default, the script installs the
|
|
<a href="https://metabarcoding.org/obitools4"><abbr title="The fourth version of the OBITools, a set of unix command line tools for manipulating DNA metabarcoding data">OBITools4</abbr>
|
|
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</a> commands and other associated files into the <code>/usr/local</code> directory. The names of the commands in the new
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<a href="https://metabarcoding.org/obitools4"><abbr title="The fourth version of the OBITools, a set of unix command line tools for manipulating DNA metabarcoding data">OBITools4</abbr>
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</a> are mostly identical to those in previous <abbr title="A set of unix command line tools for manipulating DNA metabarcoding data">OBITools</abbr>
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. Therefore, installing the new <abbr title="A set of unix command line tools for manipulating DNA metabarcoding data">OBITools</abbr>
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may hide or delete the old ones. If you want both versions to be available on your system, the installation script offers two options:</p>
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<ul>
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<li>
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<p><code>--install-dir|-i <PATH></code>: Directory where obitools are installed (as example use <code>/usr/local</code> not <code>/usr/local/bin</code>).</p>
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</li>
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<li>
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<p><code>--obitools-prefix|-p</code>: 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 <code>-p g</code> will produce <code>gobigrep</code> command instead of <code>obigrep</code>).</p>
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</li>
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</ul>
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<p>You can use these options by following the installation command:</p>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-bash" data-lang="bash"><span style="display:flex;"><span>curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | <span style="color:#ae81ff">\
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</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> bash -s -- --install-dir test_install --obitools-prefix k
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</span></span></code></pre></div><p>In this case, the binaries will be installed in the <code>test_install</code> directory and all command names will be prefixed with the letter <code>k</code>. Thus <code>obigrep</code> will be named <code>kobigrep</code>.</p>
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