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kelly-sovacool committed Aug 17, 2024
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28 changes: 25 additions & 3 deletions dev/CHANGELOG.html
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</head>

<body class="nav-fixed fullcontent">
<body class="nav-fixed">

<div id="quarto-search-results"></div>
<header id="quarto-header" class="headroom fixed-top">
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<div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
<!-- sidebar -->
<!-- margin-sidebar -->

<div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
<nav id="TOC" role="doc-toc" class="toc-active">
<h2 id="toc-title">On this page</h2>

<ul>
<li><a href="#tools-development-version" id="toc-tools-development-version" class="nav-link active" data-scroll-target="#tools-development-version">Tools development version</a></li>
<li><a href="#tools-0.0.1" id="toc-tools-0.0.1" class="nav-link" data-scroll-target="#tools-0.0.1">Tools 0.0.1</a></li>
</ul>
<div class="toc-actions"><ul><li><a href="https://github.com/CCBR/Tools/edit/main/CHANGELOG.md" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/CCBR/Tools/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
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<main class="content" id="quarto-document-content">

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}
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var mailtoRegex = new RegExp(/^mailto:/);
var filterRegex = new RegExp('/' + window.location.host + '/');
var filterRegex = new RegExp("https:\/\/ccbr\.github\.io\/Tools");
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
}
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});
</script>
</div> <!-- /content -->
<footer class="footer">
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<p>Created by the <a href="https://github.com/CCBR">CCR Collaborative Bioinformatics Resource</a></p>
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42 changes: 39 additions & 3 deletions dev/CONTRIBUTING.html
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</head>

<body class="nav-fixed fullcontent">
<body class="nav-fixed">

<div id="quarto-search-results"></div>
<header id="quarto-header" class="headroom fixed-top">
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<div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
<!-- sidebar -->
<!-- margin-sidebar -->

<div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
<nav id="TOC" role="doc-toc" class="toc-active">
<h2 id="toc-title">On this page</h2>

<ul>
<li><a href="#contributing-to-ccbr-tools" id="toc-contributing-to-ccbr-tools" class="nav-link active" data-scroll-target="#contributing-to-ccbr-tools">Contributing to CCBR Tools</a>
<ul class="collapse">
<li><a href="#proposing-changes-with-issues" id="toc-proposing-changes-with-issues" class="nav-link" data-scroll-target="#proposing-changes-with-issues">Proposing changes with issues</a></li>
<li><a href="#pull-request-process" id="toc-pull-request-process" class="nav-link" data-scroll-target="#pull-request-process">Pull request process</a>
<ul class="collapse">
<li><a href="#clone-the-repo" id="toc-clone-the-repo" class="nav-link" data-scroll-target="#clone-the-repo">Clone the repo</a></li>
<li><a href="#if-this-is-your-first-time-cloning-the-repo-you-may-need-to-install-dependencies" id="toc-if-this-is-your-first-time-cloning-the-repo-you-may-need-to-install-dependencies" class="nav-link" data-scroll-target="#if-this-is-your-first-time-cloning-the-repo-you-may-need-to-install-dependencies">If this is your first time cloning the repo, you may need to install dependencies</a></li>
<li><a href="#create-a-branch" id="toc-create-a-branch" class="nav-link" data-scroll-target="#create-a-branch">Create a branch</a></li>
<li><a href="#make-your-changes" id="toc-make-your-changes" class="nav-link" data-scroll-target="#make-your-changes">Make your changes</a></li>
<li><a href="#commit-and-push-your-changes" id="toc-commit-and-push-your-changes" class="nav-link" data-scroll-target="#commit-and-push-your-changes">Commit and push your changes</a></li>
<li><a href="#create-the-pr" id="toc-create-the-pr" class="nav-link" data-scroll-target="#create-the-pr">Create the PR</a></li>
<li><a href="#wait-for-a-maintainer-to-review-your-pr" id="toc-wait-for-a-maintainer-to-review-your-pr" class="nav-link" data-scroll-target="#wait-for-a-maintainer-to-review-your-pr">Wait for a maintainer to review your PR</a></li>
<li><a href="#after-your-pr-has-been-merged" id="toc-after-your-pr-has-been-merged" class="nav-link" data-scroll-target="#after-your-pr-has-been-merged">After your PR has been merged</a></li>
</ul></li>
<li><a href="#helpful-links-for-more-information" id="toc-helpful-links-for-more-information" class="nav-link" data-scroll-target="#helpful-links-for-more-information">Helpful links for more information</a></li>
</ul></li>
</ul>
<div class="toc-actions"><ul><li><a href="https://github.com/CCBR/Tools/edit/main/CONTRIBUTING.md" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/CCBR/Tools/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
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}
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var mailtoRegex = new RegExp(/^mailto:/);
var filterRegex = new RegExp('/' + window.location.host + '/');
var filterRegex = new RegExp("https:\/\/ccbr\.github\.io\/Tools");
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
}
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});
</script>
</div> <!-- /content -->
<footer class="footer">
<div class="nav-footer">
<div class="nav-footer-left">
<p>Created by the <a href="https://github.com/CCBR">CCR Collaborative Bioinformatics Resource</a></p>
</div>
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&nbsp;
<div class="toc-actions d-sm-block d-md-none"><ul><li><a href="https://github.com/CCBR/Tools/edit/main/CONTRIBUTING.md" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/CCBR/Tools/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div>
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41 changes: 38 additions & 3 deletions dev/index.html
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</head>

<body class="nav-fixed fullcontent">
<body class="nav-fixed">

<div id="quarto-search-results"></div>
<header id="quarto-header" class="headroom fixed-top">
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<div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
<!-- sidebar -->
<!-- margin-sidebar -->

<div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
<nav id="TOC" role="doc-toc" class="toc-active">
<h2 id="toc-title">On this page</h2>

<ul>
<li><a href="#ccbr-tools" id="toc-ccbr-tools" class="nav-link active" data-scroll-target="#ccbr-tools">CCBR Tools</a>
<ul class="collapse">
<li><a href="#installation" id="toc-installation" class="nav-link" data-scroll-target="#installation">Installation</a></li>
<li><a href="#usage" id="toc-usage" class="nav-link" data-scroll-target="#usage">Usage</a>
<ul class="collapse">
<li><a href="#cli" id="toc-cli" class="nav-link" data-scroll-target="#cli">CLI</a></li>
<li><a href="#python" id="toc-python" class="nav-link" data-scroll-target="#python">Python</a></li>
</ul></li>
<li><a href="#cli-utilities" id="toc-cli-utilities" class="nav-link" data-scroll-target="#cli-utilities">CLI Utilities</a></li>
<li><a href="#external-scripts" id="toc-external-scripts" class="nav-link" data-scroll-target="#external-scripts">External Scripts</a></li>
<li><a href="#citation" id="toc-citation" class="nav-link" data-scroll-target="#citation">Citation</a>
<ul class="collapse">
<li><a href="#bibtex-entry" id="toc-bibtex-entry" class="nav-link" data-scroll-target="#bibtex-entry">Bibtex entry</a></li>
</ul></li>
</ul></li>
</ul>
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<main class="content" id="quarto-document-content">

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}
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var mailtoRegex = new RegExp(/^mailto:/);
var filterRegex = new RegExp('/' + window.location.host + '/');
var filterRegex = new RegExp("https:\/\/ccbr\.github\.io\/Tools");
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
}
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});
</script>
</div> <!-- /content -->
<footer class="footer">
<div class="nav-footer">
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<p>Created by the <a href="https://github.com/CCBR">CCR Collaborative Bioinformatics Resource</a></p>
</div>
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&nbsp;
<div class="toc-actions d-sm-block d-md-none"><ul><li><a href="https://github.com/CCBR/Tools/edit/main/index.md" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/CCBR/Tools/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div>
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</div>
</div>
</footer>



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30 changes: 27 additions & 3 deletions dev/reference/index.html
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</head>

<body class="nav-sidebar floating nav-fixed fullcontent">
<body class="nav-sidebar floating nav-fixed">

<div id="quarto-search-results"></div>
<header id="quarto-header" class="headroom fixed-top">
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</nav>
<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
<!-- margin-sidebar -->

<div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
<nav id="TOC" role="doc-toc" class="toc-active">
<h2 id="toc-title">On this page</h2>

<ul>
<li><a href="#function-reference" id="toc-function-reference" class="nav-link active" data-scroll-target="#function-reference">Function reference</a>
<ul class="collapse">
<li><a href="#modules" id="toc-modules" class="nav-link" data-scroll-target="#modules">Modules</a></li>
</ul></li>
</ul>
<div class="toc-actions"><ul><li><a href="https://github.com/CCBR/Tools/edit/main/reference/index.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/CCBR/Tools/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
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<main class="content" id="quarto-document-content">

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}
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var mailtoRegex = new RegExp(/^mailto:/);
var filterRegex = new RegExp('/' + window.location.host + '/');
var filterRegex = new RegExp("https:\/\/ccbr\.github\.io\/Tools");
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
}
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});
</script>
</div> <!-- /content -->
<footer class="footer">
<div class="nav-footer">
<div class="nav-footer-left">
<p>Created by the <a href="https://github.com/CCBR">CCR Collaborative Bioinformatics Resource</a></p>
</div>
<div class="nav-footer-center">
&nbsp;
<div class="toc-actions d-sm-block d-md-none"><ul><li><a href="https://github.com/CCBR/Tools/edit/main/reference/index.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/CCBR/Tools/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div>
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55 changes: 52 additions & 3 deletions dev/reference/jobby.html
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</head>

<body class="nav-sidebar floating nav-fixed fullcontent">
<body class="nav-sidebar floating nav-fixed">

<div id="quarto-search-results"></div>
<header id="quarto-header" class="headroom fixed-top">
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</nav>
<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
<!-- margin-sidebar -->

<div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
<nav id="TOC" role="doc-toc" class="toc-active">
<h2 id="toc-title">On this page</h2>

<ul>
<li><a href="#ccbr_tools.jobby" id="toc-ccbr_tools.jobby" class="nav-link active" data-scroll-target="#ccbr_tools.jobby">jobby</a>
<ul class="collapse">
<li><a href="#about" id="toc-about" class="nav-link" data-scroll-target="#about">About</a></li>
<li><a href="#requires" id="toc-requires" class="nav-link" data-scroll-target="#requires">Requires</a></li>
<li><a href="#disclaimer" id="toc-disclaimer" class="nav-link" data-scroll-target="#disclaimer">Disclaimer</a></li>
<li><a href="#usage" id="toc-usage" class="nav-link" data-scroll-target="#usage">Usage</a></li>
<li><a href="#example" id="toc-example" class="nav-link" data-scroll-target="#example">Example</a></li>
<li><a href="#classes" id="toc-classes" class="nav-link" data-scroll-target="#classes">Classes</a>
<ul class="collapse">
<li><a href="#ccbr_tools.jobby.Colors" id="toc-ccbr_tools.jobby.Colors" class="nav-link" data-scroll-target="#ccbr_tools.jobby.Colors">Colors</a></li>
</ul></li>
<li><a href="#functions" id="toc-functions" class="nav-link" data-scroll-target="#functions">Functions</a>
<ul class="collapse">
<li><a href="#ccbr_tools.jobby.add_missing" id="toc-ccbr_tools.jobby.add_missing" class="nav-link" data-scroll-target="#ccbr_tools.jobby.add_missing">add_missing</a></li>
<li><a href="#ccbr_tools.jobby.convert_size" id="toc-ccbr_tools.jobby.convert_size" class="nav-link" data-scroll-target="#ccbr_tools.jobby.convert_size">convert_size</a></li>
<li><a href="#ccbr_tools.jobby.dashboard_cli" id="toc-ccbr_tools.jobby.dashboard_cli" class="nav-link" data-scroll-target="#ccbr_tools.jobby.dashboard_cli">dashboard_cli</a></li>
<li><a href="#ccbr_tools.jobby.err" id="toc-ccbr_tools.jobby.err" class="nav-link" data-scroll-target="#ccbr_tools.jobby.err">err</a></li>
<li><a href="#ccbr_tools.jobby.fatal" id="toc-ccbr_tools.jobby.fatal" class="nav-link" data-scroll-target="#ccbr_tools.jobby.fatal">fatal</a></li>
<li><a href="#ccbr_tools.jobby.get_toolkit" id="toc-ccbr_tools.jobby.get_toolkit" class="nav-link" data-scroll-target="#ccbr_tools.jobby.get_toolkit">get_toolkit</a></li>
<li><a href="#ccbr_tools.jobby.jobby" id="toc-ccbr_tools.jobby.jobby" class="nav-link" data-scroll-target="#ccbr_tools.jobby.jobby">jobby</a></li>
<li><a href="#ccbr_tools.jobby.parsed_arguments" id="toc-ccbr_tools.jobby.parsed_arguments" class="nav-link" data-scroll-target="#ccbr_tools.jobby.parsed_arguments">parsed_arguments</a></li>
<li><a href="#ccbr_tools.jobby.sacct" id="toc-ccbr_tools.jobby.sacct" class="nav-link" data-scroll-target="#ccbr_tools.jobby.sacct">sacct</a></li>
<li><a href="#ccbr_tools.jobby.sge" id="toc-ccbr_tools.jobby.sge" class="nav-link" data-scroll-target="#ccbr_tools.jobby.sge">sge</a></li>
<li><a href="#ccbr_tools.jobby.slurm" id="toc-ccbr_tools.jobby.slurm" class="nav-link" data-scroll-target="#ccbr_tools.jobby.slurm">slurm</a></li>
<li><a href="#ccbr_tools.jobby.to_bytes" id="toc-ccbr_tools.jobby.to_bytes" class="nav-link" data-scroll-target="#ccbr_tools.jobby.to_bytes">to_bytes</a></li>
<li><a href="#ccbr_tools.jobby.uge" id="toc-ccbr_tools.jobby.uge" class="nav-link" data-scroll-target="#ccbr_tools.jobby.uge">uge</a></li>
<li><a href="#ccbr_tools.jobby.which" id="toc-ccbr_tools.jobby.which" class="nav-link" data-scroll-target="#ccbr_tools.jobby.which">which</a></li>
</ul></li>
</ul></li>
</ul>
<div class="toc-actions"><ul><li><a href="https://github.com/CCBR/Tools/edit/main/reference/jobby.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/CCBR/Tools/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
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}
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var mailtoRegex = new RegExp(/^mailto:/);
var filterRegex = new RegExp('/' + window.location.host + '/');
var filterRegex = new RegExp("https:\/\/ccbr\.github\.io\/Tools");
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
}
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});
</script>
</div> <!-- /content -->
<footer class="footer">
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<p>Created by the <a href="https://github.com/CCBR">CCR Collaborative Bioinformatics Resource</a></p>
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