1491 lines
42 KiB
HTML
1491 lines
42 KiB
HTML
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<!doctype html>
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<html lang="en" class="no-js">
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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">
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<link rel="canonical" href="https://www.rapids.science/setup/installation/">
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<link rel="icon" href="../../assets/images/favicon.png">
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<meta name="generator" content="mkdocs-1.1.2, mkdocs-material-7.0.7+insiders-2.4.0">
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<title>Installation - RAPIDS</title>
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<link rel="stylesheet" href="../../assets/stylesheets/main.ec3b3678.min.css">
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<link rel="stylesheet" href="../../assets/stylesheets/palette.de2705de.min.css">
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<link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
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<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:300,400,400i,700%7CRoboto+Mono&display=fallback">
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<style>:root{--md-text-font-family:"Roboto";--md-code-font-family:"Roboto Mono"}</style>
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<link rel="stylesheet" href="../../stylesheets/extra.css">
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</head>
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<body dir="ltr" data-md-color-scheme="default" data-md-color-primary="blue" data-md-color-accent="blue">
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<script>function __prefix(e){return new URL("../..",location).pathname+"."+e}function __get(e,t=localStorage){return JSON.parse(t.getItem(__prefix(e)))}</script>
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<script>var palette=__get("__palette");if(null!==palette&&"object"==typeof palette.color)for(var key in palette.color)document.body.setAttribute("data-md-color-"+key,palette.color[key])</script>
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<input class="md-toggle" data-md-toggle="drawer" type="checkbox" id="__drawer" autocomplete="off">
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<input class="md-toggle" data-md-toggle="search" type="checkbox" id="__search" autocomplete="off">
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<label class="md-overlay" for="__drawer"></label>
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<div data-md-component="skip">
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<a href="#installation" class="md-skip">
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Skip to content
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</a>
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</div>
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<div data-md-component="announce">
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</div>
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<div data-md-component="outdated" hidden>
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<aside class="md-banner md-banner--warning">
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<div class="md-banner__inner md-grid md-typeset">
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You're not viewing the latest stable version of RAPIDS.
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<a href="https://www.rapids.science/">
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<strong> Click here to go to latest. </strong>
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</a>
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</div>
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<script>var el=document.querySelector("[data-md-component=outdated]"),outdated=__get("__outdated",sessionStorage);!0===outdated&&el&&(el.hidden=!1)</script>
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</aside>
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</div>
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<header class="md-header" data-md-component="header">
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<nav class="md-header__inner md-grid" aria-label="Header">
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<a href="../.." title="RAPIDS" class="md-header__button md-logo" aria-label="RAPIDS" data-md-component="logo">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M19 18.31V20a2 2 0 0 1-2 2H7a2 2 0 0 1-2-2v-3.7c-.46-.18-1.05-.3-2-.3a1 1 0 0 1-1-1 1 1 0 0 1 1-1c.82 0 1.47.08 2 .21V12.3c-.46-.18-1.05-.3-2-.3a1 1 0 0 1-1-1 1 1 0 0 1 1-1c.82 0 1.47.08 2 .21V8.3C4.54 8.12 3.95 8 3 8a1 1 0 0 1-1-1 1 1 0 0 1 1-1c.82 0 1.47.08 2 .21V4a2 2 0 0 1 2-2h10a2 2 0 0 1 2 2v2.16c1.78.31 2.54.97 2.71 1.13.39.39.39 1.03 0 1.42-.39.39-.91.38-1.42 0 0 0-1.04-.71-3.29-.71-1.26 0-2.09.41-3.05.9-1.04.51-2.21 1.1-3.95 1.1-.36 0-.69 0-1-.04V7.95c.3.05.63.05 1 .05 1.26 0 2.09-.41 3.05-.89C14.09 6.59 15.27 6 17 6V4H7v16h10v-2c1.5 0 1.97.29 2 .31M17 10c-1.73 0-2.91.59-3.95 1.11-.96.48-1.79.89-3.05.89-.37 0-.7 0-1-.05v2.01c.31.04.64.04 1 .04 1.74 0 2.91-.59 3.95-1.1.96-.48 1.79-.9 3.05-.9 2.25 0 3.29.71 3.29.71.51.39 1.03.39 1.42 0 .39-.39.39-1.02 0-1.42C21.5 11.08 20.25 10 17 10m0 4c-1.73 0-2.91.59-3.95 1.11-.96.48-1.79.89-3.05.89-.37 0-.7 0-1-.05v2.01c.31.04.64.04 1 .04 1.74 0 2.91-.59 3.95-1.1.96-.48 1.79-.9 3.05-.9 2.25 0 3.29.71 3.29.71.51.39 1.03.39 1.42 0 .39-.39.39-1.02 0-1.42C21.5 15.08 20.25 14 17 14z"/></svg>
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</a>
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<label class="md-header__button md-icon" for="__drawer">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M3 6h18v2H3V6m0 5h18v2H3v-2m0 5h18v2H3v-2z"/></svg>
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</label>
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<div class="md-header__title" data-md-component="header-title">
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<div class="md-header__ellipsis">
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<div class="md-header__topic">
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<span class="md-ellipsis">
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RAPIDS
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</span>
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</div>
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<div class="md-header__topic" data-md-component="header-topic">
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<span class="md-ellipsis">
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Installation
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</span>
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</div>
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</div>
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</div>
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<form class="md-header__option" data-md-component="palette">
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<input class="md-option" data-md-color-media="" data-md-color-scheme="default" data-md-color-primary="blue" data-md-color-accent="blue" type="radio" name="__palette" id="__palette_1">
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<label class="md-header__button md-icon" title="Switch to light mode" for="__palette_2" hidden>
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M17 7H7a5 5 0 0 0-5 5 5 5 0 0 0 5 5h10a5 5 0 0 0 5-5 5 5 0 0 0-5-5m0 8a3 3 0 0 1-3-3 3 3 0 0 1 3-3 3 3 0 0 1 3 3 3 3 0 0 1-3 3z"/></svg>
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</label>
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<input class="md-option" data-md-color-media="" data-md-color-scheme="slate" data-md-color-primary="blue" data-md-color-accent="blue" type="radio" name="__palette" id="__palette_2">
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<label class="md-header__button md-icon" title="Switch to dark mode" for="__palette_1" hidden>
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M7 10a2 2 0 0 1 2 2 2 2 0 0 1-2 2 2 2 0 0 1-2-2 2 2 0 0 1 2-2m10-3a5 5 0 0 1 5 5 5 5 0 0 1-5 5H7a5 5 0 0 1-5-5 5 5 0 0 1 5-5h10M7 9a3 3 0 0 0-3 3 3 3 0 0 0 3 3h10a3 3 0 0 0 3-3 3 3 0 0 0-3-3H7z"/></svg>
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</label>
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</form>
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<label class="md-header__button md-icon" for="__search">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M9.5 3A6.5 6.5 0 0 1 16 9.5c0 1.61-.59 3.09-1.56 4.23l.27.27h.79l5 5-1.5 1.5-5-5v-.79l-.27-.27A6.516 6.516 0 0 1 9.5 16 6.5 6.5 0 0 1 3 9.5 6.5 6.5 0 0 1 9.5 3m0 2C7 5 5 7 5 9.5S7 14 9.5 14 14 12 14 9.5 12 5 9.5 5z"/></svg>
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</label>
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<div class="md-search" data-md-component="search" role="dialog">
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<label class="md-search__overlay" for="__search"></label>
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<div class="md-search__inner" role="search">
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<form class="md-search__form" name="search">
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<input type="text" class="md-search__input" name="query" aria-label="Search" placeholder="Search" autocapitalize="off" autocorrect="off" autocomplete="off" spellcheck="false" data-md-component="search-query" required>
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<label class="md-search__icon md-icon" for="__search">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M9.5 3A6.5 6.5 0 0 1 16 9.5c0 1.61-.59 3.09-1.56 4.23l.27.27h.79l5 5-1.5 1.5-5-5v-.79l-.27-.27A6.516 6.516 0 0 1 9.5 16 6.5 6.5 0 0 1 3 9.5 6.5 6.5 0 0 1 9.5 3m0 2C7 5 5 7 5 9.5S7 14 9.5 14 14 12 14 9.5 12 5 9.5 5z"/></svg>
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M20 11v2H8l5.5 5.5-1.42 1.42L4.16 12l7.92-7.92L13.5 5.5 8 11h12z"/></svg>
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</label>
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<nav class="md-search__options" aria-label="Search">
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<button type="reset" class="md-search__icon md-icon" aria-label="Clear" tabindex="-1">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M19 6.41 17.59 5 12 10.59 6.41 5 5 6.41 10.59 12 5 17.59 6.41 19 12 13.41 17.59 19 19 17.59 13.41 12 19 6.41z"/></svg>
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</button>
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</nav>
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<div class="md-search__suggest" data-md-component="search-suggest"></div>
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</form>
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<div class="md-search__output">
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<div class="md-search__scrollwrap" data-md-scrollfix>
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<div class="md-search-result" data-md-component="search-result">
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<div class="md-search-result__meta">
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Initializing search
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</div>
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<ol class="md-search-result__list"></ol>
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</div>
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</div>
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</div>
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</div>
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</div>
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<div class="md-header__source">
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<a href="https://github.com/carissalow/rapids/" title="Go to repository" class="md-source" data-md-component="source">
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<div class="md-source__icon md-icon">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
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</div>
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<div class="md-source__repository">
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carissalow/rapids
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</div>
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</a>
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</div>
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</nav>
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</header>
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<div class="md-container" data-md-component="container">
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<main class="md-main" data-md-component="main">
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<div class="md-main__inner md-grid">
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<div class="md-sidebar md-sidebar--primary" data-md-component="sidebar" data-md-type="navigation" >
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<div class="md-sidebar__scrollwrap">
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<div class="md-sidebar__inner">
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<nav class="md-nav md-nav--primary" aria-label="Navigation" data-md-level="0">
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<label class="md-nav__title" for="__drawer">
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<a href="../.." title="RAPIDS" class="md-nav__button md-logo" aria-label="RAPIDS" data-md-component="logo">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M19 18.31V20a2 2 0 0 1-2 2H7a2 2 0 0 1-2-2v-3.7c-.46-.18-1.05-.3-2-.3a1 1 0 0 1-1-1 1 1 0 0 1 1-1c.82 0 1.47.08 2 .21V12.3c-.46-.18-1.05-.3-2-.3a1 1 0 0 1-1-1 1 1 0 0 1 1-1c.82 0 1.47.08 2 .21V8.3C4.54 8.12 3.95 8 3 8a1 1 0 0 1-1-1 1 1 0 0 1 1-1c.82 0 1.47.08 2 .21V4a2 2 0 0 1 2-2h10a2 2 0 0 1 2 2v2.16c1.78.31 2.54.97 2.71 1.13.39.39.39 1.03 0 1.42-.39.39-.91.38-1.42 0 0 0-1.04-.71-3.29-.71-1.26 0-2.09.41-3.05.9-1.04.51-2.21 1.1-3.95 1.1-.36 0-.69 0-1-.04V7.95c.3.05.63.05 1 .05 1.26 0 2.09-.41 3.05-.89C14.09 6.59 15.27 6 17 6V4H7v16h10v-2c1.5 0 1.97.29 2 .31M17 10c-1.73 0-2.91.59-3.95 1.11-.96.48-1.79.89-3.05.89-.37 0-.7 0-1-.05v2.01c.31.04.64.04 1 .04 1.74 0 2.91-.59 3.95-1.1.96-.48 1.79-.9 3.05-.9 2.25 0 3.29.71 3.29.71.51.39 1.03.39 1.42 0 .39-.39.39-1.02 0-1.42C21.5 11.08 20.25 10 17 10m0 4c-1.73 0-2.91.59-3.95 1.11-.96.48-1.79.89-3.05.89-.37 0-.7 0-1-.05v2.01c.31.04.64.04 1 .04 1.74 0 2.91-.59 3.95-1.1.96-.48 1.79-.9 3.05-.9 2.25 0 3.29.71 3.29.71.51.39 1.03.39 1.42 0 .39-.39.39-1.02 0-1.42C21.5 15.08 20.25 14 17 14z"/></svg>
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</a>
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RAPIDS
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</label>
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<div class="md-nav__source">
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<a href="https://github.com/carissalow/rapids/" title="Go to repository" class="md-source" data-md-component="source">
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<div class="md-source__icon md-icon">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
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</div>
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<div class="md-source__repository">
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carissalow/rapids
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</div>
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</a>
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</div>
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
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<a href="../.." class="md-nav__link">
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Home
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</a>
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</li>
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<li class="md-nav__item md-nav__item--active md-nav__item--section md-nav__item--nested">
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<input class="md-nav__toggle md-toggle" data-md-toggle="__nav_2" type="checkbox" id="__nav_2" checked>
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<label class="md-nav__link" for="__nav_2">
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Setup
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<span class="md-nav__icon md-icon"></span>
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</label>
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<nav class="md-nav" aria-label="Setup" data-md-level="1">
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<label class="md-nav__title" for="__nav_2">
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<span class="md-nav__icon md-icon"></span>
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Setup
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
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<a href="../../file-structure/" class="md-nav__link">
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File Structure
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</a>
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</li>
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<li class="md-nav__item md-nav__item--active">
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<input class="md-nav__toggle md-toggle" data-md-toggle="toc" type="checkbox" id="__toc">
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<a href="./" class="md-nav__link md-nav__link--active">
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Installation
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../configuration/" class="md-nav__link">
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Configuration
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../execution/" class="md-nav__link">
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Execution
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</a>
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</li>
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</ul>
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</nav>
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
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<input class="md-nav__toggle md-toggle" data-md-toggle="__nav_3" type="checkbox" id="__nav_3" >
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<label class="md-nav__link" for="__nav_3">
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Example Workflows
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<span class="md-nav__icon md-icon"></span>
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</label>
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<nav class="md-nav" aria-label="Example Workflows" data-md-level="1">
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<label class="md-nav__title" for="__nav_3">
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<span class="md-nav__icon md-icon"></span>
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Example Workflows
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
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<a href="../../workflow-examples/minimal/" class="md-nav__link">
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Minimal
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</a>
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</li>
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<div class="md-sidebar__inner">
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<div class="md-content" data-md-component="content">
|
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<article class="md-content__inner md-typeset">
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<a href="https://github.com/carissalow/rapids/edit/master/docs/setup/installation.md" title="Edit this page" class="md-content__button md-icon">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M20.71 7.04c.39-.39.39-1.04 0-1.41l-2.34-2.34c-.37-.39-1.02-.39-1.41 0l-1.84 1.83 3.75 3.75M3 17.25V21h3.75L17.81 9.93l-3.75-3.75L3 17.25z"/></svg>
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</a>
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<h1 id="installation">Installation<a class="headerlink" href="#installation" title="Permanent link">¶</a></h1>
|
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<p>You can install RAPIDS using Docker (the fastest), or native instructions for MacOS and Linux (Ubuntu). Windows is supported through Docker or WSL.</p>
|
|
<div class="tabbed-set" data-tabs="1:4"><input checked="checked" id="__tabbed_1_1" name="__tabbed_1" type="radio" /><label for="__tabbed_1_1">Docker</label><div class="tabbed-content">
|
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<ol>
|
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<li>
|
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<p>Install <a href="https://docs.docker.com/desktop/">Docker</a></p>
|
|
</li>
|
|
<li>
|
|
<p>Pull our RAPIDS container
|
|
<div class="highlight"><pre><span></span><code>docker pull moshiresearch/rapids:latest
|
|
</code></pre></div></p>
|
|
</li>
|
|
<li>
|
|
<p>Run RAPIDS' container (after this step is done you should see a
|
|
prompt in the main RAPIDS folder with its python environment active)</p>
|
|
<div class="highlight"><pre><span></span><code>docker run -it moshiresearch/rapids:latest
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Pull the latest version of RAPIDS</p>
|
|
<div class="highlight"><pre><span></span><code>git pull
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Make RAPIDS script executable
|
|
<div class="highlight"><pre><span></span><code>chmod +x rapids
|
|
</code></pre></div></p>
|
|
</li>
|
|
<li>
|
|
<p>Check that RAPIDS is working
|
|
<div class="highlight"><pre><span></span><code>./rapids -j1
|
|
</code></pre></div></p>
|
|
</li>
|
|
<li>
|
|
<p><em>Optional</em>. You can edit RAPIDS files with <code>vim</code> but we recommend using <code>Visual Studio Code</code> and its <code>Remote Containers</code> extension</p>
|
|
<details class="info"><summary>How to configure Remote Containers extension</summary><ul>
|
|
<li>Make sure RAPIDS container is running<ul>
|
|
<li>Install the <a href="https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers">Remote - Containers extension</a></li>
|
|
<li>Go to the <code>Remote Explorer</code> panel on the left hand sidebar</li>
|
|
<li>On the top right dropdown menu choose <code>Containers</code></li>
|
|
<li>Double click on the <code>moshiresearch/rapids</code> container in the<code>CONTAINERS</code> tree</li>
|
|
<li>A new VS Code session should open on RAPIDS main folder inside the container.</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</details>
|
|
</li>
|
|
</ol>
|
|
<div class="admonition warning">
|
|
<p class="admonition-title">Warning</p>
|
|
<p>If you installed RAPIDS using Docker for Windows on Windows 10, the container will have <a href="https://stackoverflow.com/questions/43460770/docker-windows-container-memory-limit">limits</a> on the amount of RAM it can use. If you find that RAPIDS crashes due to running out of memory, <a href="https://stackoverflow.com/a/56583203/6030343">increase</a> this limit.</p>
|
|
</div>
|
|
</div>
|
|
<input id="__tabbed_1_2" name="__tabbed_1" type="radio" /><label for="__tabbed_1_2">MacOS</label><div class="tabbed-content">
|
|
<p>We tested these instructions in Catalina</p>
|
|
<ol>
|
|
<li>
|
|
<p>Install <a href="https://brew.sh/">brew</a></p>
|
|
</li>
|
|
<li>
|
|
<p>Install MySQL</p>
|
|
<div class="highlight"><pre><span></span><code>brew install mysql
|
|
brew services start mysql
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install R 4.0, pandoc and rmarkdown. If you have other instances of R, we recommend uninstalling them</p>
|
|
<div class="highlight"><pre><span></span><code>brew install r
|
|
brew install pandoc
|
|
Rscript --vanilla -e <span class="s1">'install.packages("rmarkdown", repos="http://cran.us.r-project.org")'</span>
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install miniconda (restart your terminal afterwards)</p>
|
|
<div class="highlight"><pre><span></span><code>brew cask install miniconda
|
|
conda init zsh <span class="c1"># (or conda init bash)</span>
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Clone our repo</p>
|
|
<div class="highlight"><pre><span></span><code>git clone https://github.com/carissalow/rapids
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Create a python virtual environment</p>
|
|
<div class="highlight"><pre><span></span><code><span class="nb">cd</span> rapids
|
|
conda env create -f environment.yml -n rapids
|
|
conda activate rapids
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install R packages and virtual environment:</p>
|
|
<div class="highlight"><pre><span></span><code>snakemake -j1 renv_install
|
|
snakemake -j1 renv_restore
|
|
</code></pre></div>
|
|
<div class="admonition note">
|
|
<p class="admonition-title">Note<p>This step could take several minutes to complete, especially if you have less than 3Gb of RAM or packages need to be compiled from source. Please be patient and let it run until completion.</p>
|
|
</p>
|
|
</div>
|
|
</li>
|
|
<li>
|
|
<p>Make RAPIDS script executable
|
|
<div class="highlight"><pre><span></span><code>chmod +x rapids
|
|
</code></pre></div></p>
|
|
</li>
|
|
<li>
|
|
<p>Check that RAPIDS is working
|
|
<div class="highlight"><pre><span></span><code>./rapids -j1
|
|
</code></pre></div></p>
|
|
</li>
|
|
</ol>
|
|
</div>
|
|
<input id="__tabbed_1_3" name="__tabbed_1" type="radio" /><label for="__tabbed_1_3">Ubuntu</label><div class="tabbed-content">
|
|
<p>We tested RAPIDS on Ubuntu 18.04 & 20.04. Note that the necessary Python and R packages are available in other Linux distributions, so if you decide to give it a try, let us know and we can update these docs.</p>
|
|
<ol>
|
|
<li>
|
|
<p>Install dependencies</p>
|
|
<div class="highlight"><pre><span></span><code>sudo apt install libcurl4-openssl-dev
|
|
sudo apt install libssl-dev
|
|
sudo apt install libxml2-dev
|
|
sudo apt install libglpk40
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install MySQL</p>
|
|
<div class="highlight"><pre><span></span><code>sudo apt install libmysqlclient-dev
|
|
sudo apt install mysql-server
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Add key for R’s repository.</p>
|
|
<div class="highlight"><pre><span></span><code>sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Add R’s repository</p>
|
|
<div class="tabbed-set" data-tabs="2:2"><input checked="checked" id="__tabbed_2_1" name="__tabbed_2" type="radio" /><label for="__tabbed_2_1">Ubuntu 18.04 Bionic</label><div class="tabbed-content">
|
|
<div class="highlight"><pre><span></span><code>sudo add-apt-repository <span class="s1">'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/'</span>
|
|
</code></pre></div>
|
|
</div>
|
|
<input id="__tabbed_2_2" name="__tabbed_2" type="radio" /><label for="__tabbed_2_2">Ubuntu 20.04 Focal</label><div class="tabbed-content">
|
|
<div class="highlight"><pre><span></span><code>sudo add-apt-repository <span class="s1">'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'</span>
|
|
</code></pre></div>
|
|
</div>
|
|
</div>
|
|
</li>
|
|
<li>
|
|
<p>Install R 4.0. If you have other instances of R, we recommend uninstalling them</p>
|
|
<div class="highlight"><pre><span></span><code>sudo apt update
|
|
sudo apt install r-base
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install Pandoc and rmarkdown</p>
|
|
<div class="highlight"><pre><span></span><code>sudo apt install pandoc
|
|
Rscript --vanilla -e <span class="s1">'install.packages("rmarkdown", repos="http://cran.us.r-project.org")'</span>
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install git</p>
|
|
<div class="highlight"><pre><span></span><code>sudo apt install git
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install <a href="https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html">miniconda</a></p>
|
|
</li>
|
|
<li>
|
|
<p>Restart your current shell</p>
|
|
</li>
|
|
<li>
|
|
<p>Clone our repo:</p>
|
|
<div class="highlight"><pre><span></span><code>git clone https://github.com/carissalow/rapids
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Create a python virtual environment:</p>
|
|
<div class="highlight"><pre><span></span><code><span class="nb">cd</span> rapids
|
|
conda env create -f environment.yml -n MY_ENV_NAME
|
|
conda activate MY_ENV_NAME
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install the R virtual environment management package (renv)</p>
|
|
<div class="highlight"><pre><span></span><code>snakemake -j1 renv_install
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Restore the R virtual environment</p>
|
|
<div class="tabbed-set" data-tabs="3:3"><input checked="checked" id="__tabbed_3_1" name="__tabbed_3" type="radio" /><label for="__tabbed_3_1">Ubuntu 18.04 Bionic (fast)</label><div class="tabbed-content">
|
|
<p>Run the following command to restore the R virtual environment using <a href="https://packagemanager.rstudio.com/client/#/repos/1/overview">RSPM</a> binaries
|
|
<div class="highlight"><pre><span></span><code>R -e <span class="s1">'renv::restore(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/bionic/latest"))'</span>
|
|
</code></pre></div></p>
|
|
</div>
|
|
<input id="__tabbed_3_2" name="__tabbed_3" type="radio" /><label for="__tabbed_3_2">Ubuntu 20.04 Focal (fast)</label><div class="tabbed-content">
|
|
<p>Run the following command to restore the R virtual environment using <a href="https://packagemanager.rstudio.com/client/#/repos/1/overview">RSPM</a> binaries
|
|
<div class="highlight"><pre><span></span><code>R -e <span class="s1">'renv::restore(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/focal/latest"))'</span>
|
|
</code></pre></div></p>
|
|
</div>
|
|
<input id="__tabbed_3_3" name="__tabbed_3" type="radio" /><label for="__tabbed_3_3">Ubuntu (slow)</label><div class="tabbed-content">
|
|
<p>If the fast installation command failed for some reason, you can restore the R virtual environment from source:
|
|
<div class="highlight"><pre><span></span><code>R -e <span class="s1">'renv::restore()'</span>
|
|
</code></pre></div></p>
|
|
</div>
|
|
</div>
|
|
<div class="admonition note">
|
|
<p class="admonition-title">Note<p>This step could take several minutes to complete, especially if you have less than 3Gb of RAM or packages need to be compiled from source. Please be patient and let it run until completion.</p>
|
|
</p>
|
|
</div>
|
|
</li>
|
|
<li>
|
|
<p>Make RAPIDS script executable
|
|
<div class="highlight"><pre><span></span><code>chmod +x rapids
|
|
</code></pre></div></p>
|
|
</li>
|
|
<li>
|
|
<p>Check that RAPIDS is working
|
|
<div class="highlight"><pre><span></span><code>./rapids -j1
|
|
</code></pre></div></p>
|
|
</li>
|
|
</ol>
|
|
</div>
|
|
<input id="__tabbed_1_4" name="__tabbed_1" type="radio" /><label for="__tabbed_1_4">Windows</label><div class="tabbed-content">
|
|
<p>There are several options varying in complexity:</p>
|
|
<ul>
|
|
<li>You can use our Docker instructions (tested)</li>
|
|
<li>You can use our Ubuntu 20.04 instructions on <a href="https://docs.microsoft.com/en-us/windows/wsl/install-win10">WSL2</a> (not tested but it will likely work)</li>
|
|
<li>Native installation (experimental). If you would like to contribute to RAPIDS you could try to install MySQL, miniconda, Python, and R 4.0+ in Windows and restore the Python and R virtual environments using steps 6 and 7 of the instructions for Mac. You can <a href="../../team">get in touch</a> if you would like to discuss this with the team.</li>
|
|
</ul>
|
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</div>
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</div>
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