Mercurial > repos > johnheap > vapper
changeset 15:597fe882966e draft
Uploaded
| author | johnheap |
|---|---|
| date | Mon, 03 Jun 2019 15:57:59 -0400 |
| parents | 7d1f86b4718d |
| children | c4e87b277576 |
| files | README.md |
| diffstat | 1 files changed, 13 insertions(+), 831 deletions(-) [+] |
line wrap: on
line diff
--- a/README.md Mon Jun 03 15:56:10 2019 -0400 +++ b/README.md Mon Jun 03 15:57:59 2019 -0400 @@ -1,842 +1,24 @@ - - - - - - -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> - <link rel="dns-prefetch" href="https://github.githubassets.com"> - <link rel="dns-prefetch" href="https://avatars0.githubusercontent.com"> - <link rel="dns-prefetch" href="https://avatars1.githubusercontent.com"> - <link rel="dns-prefetch" href="https://avatars2.githubusercontent.com"> - <link rel="dns-prefetch" href="https://avatars3.githubusercontent.com"> - <link rel="dns-prefetch" href="https://github-cloud.s3.amazonaws.com"> - <link rel="dns-prefetch" href="https://user-images.githubusercontent.com/"> - - - - <link crossorigin="anonymous" media="all" integrity="sha512-3+HOqCwtQal5hOJQ+mdxiq5zmGOTjF6RhjDsPLxbKDYgGlLFeCwzoIanb7j5IiCuXKUqyC2q8FdkC4nmx2P2rA==" rel="stylesheet" href="https://github.githubassets.com/assets/frameworks-a2fba223d5af91496cac70d4ec3624df.css" /> - <link crossorigin="anonymous" media="all" integrity="sha512-MRlTIqIyb8caK5+o8llXVntXovciHyAM4qE3kWU2S7SIjAPDxYp4mE0jQp4kP5UYegy+lG9y1I6VlsdzEjb5Qw==" rel="stylesheet" href="https://github.githubassets.com/assets/site-294181adec18ed639e160b96b45d17ac.css" /> - <link crossorigin="anonymous" media="all" integrity="sha512-XjvAy/mMWN5aOA+pyb/FgAgcVgJkPkwTCwvFK07Ez/H44lvl55ZLGwtpyL4MaMrwDE8QYO+1VYljKFjqr4/iJA==" rel="stylesheet" href="https://github.githubassets.com/assets/github-5b066aa36cc405c9cbcbadf1bde399ed.css" /> - - - - - - <meta name="viewport" content="width=device-width"> - - <title>VAPPER-Galaxy/README.md at master · johnheap/VAPPER-Galaxy · GitHub</title> - <meta name="description" content="Contribute to johnheap/VAPPER-Galaxy development by creating an account on GitHub."> - <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub"> - <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub"> - <meta property="fb:app_id" content="1401488693436528"> - - <meta name="twitter:image:src" content="https://avatars0.githubusercontent.com/u/24318980?s=400&v=4" /><meta name="twitter:site" content="@github" /><meta name="twitter:card" content="summary" /><meta name="twitter:title" content="johnheap/VAPPER-Galaxy" /><meta name="twitter:description" content="Contribute to johnheap/VAPPER-Galaxy development by creating an account on GitHub." /> - <meta property="og:image" content="https://avatars0.githubusercontent.com/u/24318980?s=400&v=4" /><meta property="og:site_name" content="GitHub" /><meta property="og:type" content="object" /><meta property="og:title" content="johnheap/VAPPER-Galaxy" /><meta property="og:url" content="https://github.com/johnheap/VAPPER-Galaxy" /><meta property="og:description" content="Contribute to johnheap/VAPPER-Galaxy development by creating an account on GitHub." /> - - <link rel="assets" href="https://github.githubassets.com/"> - - <meta name="pjax-timeout" content="1000"> - - <meta name="request-id" content="A685:3C8B:6E284:CA64B:5CF5611F" data-pjax-transient> +This is the repository associated with the VAPPER Galaxy Tool available in the Galaxy Toolshed +VAPP accurately quantifies the variant antigen diversity in Trypanosoma congolense isolates or the variable Cog presence in T.vivax isolates - - - <meta name="selected-link" value="repo_source" data-pjax-transient> - - <meta name="google-site-verification" content="KT5gs8h0wvaagLKAVWq8bbeNwnZZK1r1XQysX3xurLU"> - <meta name="google-site-verification" content="ZzhVyEFwb7w3e0-uOTltm8Jsck2F5StVihD0exw2fsA"> - <meta name="google-site-verification" content="GXs5KoUUkNCoaAZn7wPN-t01Pywp9M3sEjnt_3_ZWPc"> - - <meta name="octolytics-host" content="collector.githubapp.com" /><meta name="octolytics-app-id" content="github" /><meta name="octolytics-event-url" content="https://collector.githubapp.com/github-external/browser_event" /><meta name="octolytics-dimension-request_id" content="A685:3C8B:6E284:CA64B:5CF5611F" /><meta name="octolytics-dimension-region_edge" content="iad" /><meta name="octolytics-dimension-region_render" content="iad" /> -<meta name="analytics-location" content="/<user-name>/<repo-name>/blob/show" data-pjax-transient="true" /> - +The Trypanosoma congolense variant antigen repertoire is divided into 15 clades or phylotypes. These phylotypes are present in any T. congolense isolate, but their relative abundance varies between strains. The purpose of the VAPPER is to accurately quantify antigen diversity in any T. congolense isolate by calculating the relative frequency of each phylotype. - - <meta name="google-analytics" content="UA-3769691-2"> - - -<meta class="js-ga-set" name="dimension1" content="Logged Out"> - - - - - - <meta name="hostname" content="github.com"> - <meta name="user-login" content=""> +The Galaxy VAPPER Tool has four modes. +1) T.congolense Genomic: +This takes raw NGS reads (or pre-assmebled contigs) as input, assembles them de-novo, searches for evidence of each phylotype based on hidden Markov models (HMM), and calculates their relative abundances. +The results are visualized in three different ways: a table with each phylotype and their relative frequencies as proportions of the full repertoire in the given genome; a heat map with dendogram showing either absolute VAP variation or deviation from the mean, using our pilot dataset; and a Principal Component Analysis (PCA) plot showing variation distribution in the given sample compared to our pilot dataset. - <meta name="expected-hostname" content="github.com"> - <meta name="js-proxy-site-detection-payload" content="ODM5YzU2MzYzMTk2MWVkOTNmN2U2NmQ5MDE0NWU2NzMxZWUwMGIwOGU3MjZkMDIyMTA1ZTBiZTc5YzhjNDRmM3x7InJlbW90ZV9hZGRyZXNzIjoiMTI4LjExOC4yNTAuNSIsInJlcXVlc3RfaWQiOiJBNjg1OjNDOEI6NkUyODQ6Q0E2NEI6NUNGNTYxMUYiLCJ0aW1lc3RhbXAiOjE1NTk1ODUwNTUsImhvc3QiOiJnaXRodWIuY29tIn0="> - - <meta name="enabled-features" content="UNIVERSE_BANNER,MARKETPLACE_INVOICED_BILLING,MARKETPLACE_SOCIAL_PROOF_CUSTOMERS,MARKETPLACE_TRENDING_SOCIAL_PROOF,MARKETPLACE_RECOMMENDATIONS"> - - <meta name="html-safe-nonce" content="157b876a9e4da77a240d17ea6eca7af7d5e62304"> - - <meta http-equiv="x-pjax-version" content="af1499c2254d0582d0a98af1dfd7f11b"> - - - <link href="https://github.com/johnheap/VAPPER-Galaxy/commits/master.atom" rel="alternate" title="Recent Commits to VAPPER-Galaxy:master" type="application/atom+xml"> - - <meta name="go-import" content="github.com/johnheap/VAPPER-Galaxy git https://github.com/johnheap/VAPPER-Galaxy.git"> +2) T.congolense Transcriptomic: +This requires NGS paired reads and uses bowtie2 and samtools for read mapping and processing, cufflinks for transcript abundance estimation, and hmmer for sequence identification. The output is a stacked bar chart and a table of frequencies based on the transcript abundances. - <meta name="octolytics-dimension-user_id" content="24318980" /><meta name="octolytics-dimension-user_login" content="johnheap" /><meta name="octolytics-dimension-repository_id" content="139730674" /><meta name="octolytics-dimension-repository_nwo" content="johnheap/VAPPER-Galaxy" /><meta name="octolytics-dimension-repository_public" content="true" /><meta name="octolytics-dimension-repository_is_fork" content="false" /><meta name="octolytics-dimension-repository_network_root_id" content="139730674" /><meta name="octolytics-dimension-repository_network_root_nwo" content="johnheap/VAPPER-Galaxy" /><meta name="octolytics-dimension-repository_explore_github_marketplace_ci_cta_shown" content="false" /> - - - <link rel="canonical" href="https://github.com/johnheap/VAPPER-Galaxy/blob/master/README.md" data-pjax-transient> - +3) T.vivax clusters of orthologs +The approach for T. vivax relies on the presence/absence of clusters of orthologs (COGs). It requires velvet for the genome assembly and blast. it recieves paired sequencing reads in fastq format (or a contig file if already assembled) and the output is a binary matrix of the presence/absence of each COG/gene for a given sample. Within the tool there is a database of 28 isolates that are used as a comparison producing a heatmap and dendogram. - <meta name="browser-stats-url" content="https://api.github.com/_private/browser/stats"> - - <meta name="browser-errors-url" content="https://api.github.com/_private/browser/errors"> - - <link rel="mask-icon" href="https://github.githubassets.com/pinned-octocat.svg" color="#000000"> - <link rel="icon" type="image/x-icon" class="js-site-favicon" href="https://github.githubassets.com/favicon.ico"> - -<meta name="theme-color" content="#1e2327"> +4) T.vivax Transcriptomic pathway +This method takes two NGS paired reads, maps the transcripts against a user supplied reference file and then estimates the trancript aboundance (using samtools and cufflinks). The output is then binned into 175 predefined phylotypes based on their greatest blastx similarity (this table is available in the results directory). A pident of less than 70% is considered unidentified. The results provide a tabular and graphical phylotype profile of the sample(s) - <link rel="manifest" href="/manifest.json" crossOrigin="use-credentials"> - - </head> - - <body class="logged-out env-production page-responsive page-blob"> - - - <div class="position-relative js-header-wrapper "> - <a href="#start-of-content" tabindex="1" class="px-2 py-4 bg-blue text-white show-on-focus js-skip-to-content">Skip to content</a> - <div id="js-pjax-loader-bar" class="pjax-loader-bar"><div class="progress"></div></div> - - - - - - - <header class="Header-old header-logged-out js-details-container Details position-relative f4 py-2" role="banner"> - <div class="container-lg d-lg-flex flex-items-center p-responsive"> - <div class="d-flex flex-justify-between flex-items-center"> - <a class="mr-4" href="https://github.com/" aria-label="Homepage" data-ga-click="(Logged out) Header, go to homepage, icon:logo-wordmark"> - <svg height="32" class="octicon octicon-mark-github text-white" viewBox="0 0 16 16" version="1.1" width="32" aria-hidden="true"><path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"/></svg> - </a> - - <div class="d-lg-none css-truncate css-truncate-target width-fit p-2"> - - <svg class="octicon octicon-repo" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> - <a class="Header-link" href="/johnheap">johnheap</a> - / - <a class="Header-link" href="/johnheap/VAPPER-Galaxy">VAPPER-Galaxy</a> - - - </div> - - <div class="d-flex flex-items-center"> - <a class="d-inline-block d-lg-none f5 text-white no-underline border border-gray-dark rounded-2 px-2 py-1 mr-3 mr-sm-5" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header","repository_id":null,"auth_type":"SIGN_UP","client_id":null,"originating_request_id":"A685:3C8B:6E284:CA64B:5CF5611F","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/README.md","referrer":null,"user_id":null}}" data-hydro-click-hmac="354f7bbb2f46e394f8405fc8f0214e71bdea937c5ed052854fe853b1c2dc7d56" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up" href="/join?source=header-repo"> - Sign up -</a> - <button class="btn-link d-lg-none mt-1 js-details-target" type="button" aria-label="Toggle navigation" aria-expanded="false"> - <svg height="24" class="octicon octicon-three-bars text-white" viewBox="0 0 12 16" version="1.1" width="18" aria-hidden="true"><path fill-rule="evenodd" d="M11.41 9H.59C0 9 0 8.59 0 8c0-.59 0-1 .59-1H11.4c.59 0 .59.41.59 1 0 .59 0 1-.59 1h.01zm0-4H.59C0 5 0 4.59 0 4c0-.59 0-1 .59-1H11.4c.59 0 .59.41.59 1 0 .59 0 1-.59 1h.01zM.59 11H11.4c.59 0 .59.41.59 1 0 .59 0 1-.59 1H.59C0 13 0 12.59 0 12c0-.59 0-1 .59-1z"/></svg> - </button> - </div> - </div> - - <div class="HeaderMenu HeaderMenu--logged-out position-fixed top-0 right-0 bottom-0 height-fit position-lg-relative d-lg-flex flex-justify-between flex-items-center flex-auto"> - <div class="d-flex d-lg-none flex-justify-end border-bottom bg-gray-light p-3"> - <button class="btn-link js-details-target" type="button" aria-label="Toggle navigation" aria-expanded="false"> - <svg height="24" class="octicon octicon-x text-gray" viewBox="0 0 12 16" version="1.1" width="18" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg> - </button> - </div> - - <nav class="mt-0 px-3 px-lg-0 mb-5 mb-lg-0" aria-label="Global"> - <ul class="d-lg-flex list-style-none"> - <li class="d-block d-lg-flex flex-lg-nowrap flex-lg-items-center border-bottom border-lg-bottom-0 mr-0 mr-lg-3 edge-item-fix position-relative flex-wrap flex-justify-between d-flex flex-items-center "> - <details class="HeaderMenu-details details-overlay details-reset width-full"> - <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block"> - Why GitHub? - <svg x="0px" y="0px" viewBox="0 0 14 8" xml:space="preserve" fill="none" class="icon-chevon-down-mktg position-absolute position-lg-relative"> - <path d="M1,1l6.2,6L13,1"></path> - </svg> - </summary> - <div class="dropdown-menu flex-auto rounded-1 bg-white px-0 mt-0 pb-4 p-lg-4 position-relative position-lg-absolute left-0 left-lg-n4"> - <a href="/features" class="py-2 lh-condensed-ultra d-block link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Features">Features <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a> - <ul class="list-style-none f5 pb-3"> - <li class="edge-item-fix"><a href="/features/code-review/" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Code review">Code review</a></li> - <li class="edge-item-fix"><a href="/features/project-management/" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Project management">Project management</a></li> - <li class="edge-item-fix"><a href="/features/integrations" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Integrations">Integrations</a></li> - <li class="edge-item-fix"><a href="/features/actions" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Actions">Actions</a> - <li class="edge-item-fix"><a href="/features/package-registry" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Package Registry">Package registry</a> - <li class="edge-item-fix"><a href="/features#team-management" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Team management">Team management</a></li> - <li class="edge-item-fix"><a href="/features#social-coding" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Social coding">Social coding</a></li> - <li class="edge-item-fix"><a href="/features#documentation" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Documentation">Documentation</a></li> - <li class="edge-item-fix"><a href="/features#code-hosting" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Code hosting">Code hosting</a></li> - </ul> - - <ul class="list-style-none mb-0 border-lg-top pt-lg-3"> - <li class="edge-item-fix"><a href="/customer-stories" class="py-2 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Customer stories">Customer stories <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a></li> - <li class="edge-item-fix"><a href="/security" class="py-2 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Security">Security <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a></li> - </ul> - </div> - </details> - </li> - <li class="border-bottom border-lg-bottom-0 mr-0 mr-lg-3"> - <a href="/enterprise" class="HeaderMenu-link no-underline py-3 d-block d-lg-inline-block" data-ga-click="(Logged out) Header, go to Enterprise">Enterprise</a> - </li> - - <li class="d-block d-lg-flex flex-lg-nowrap flex-lg-items-center border-bottom border-lg-bottom-0 mr-0 mr-lg-3 edge-item-fix position-relative flex-wrap flex-justify-between d-flex flex-items-center "> - <details class="HeaderMenu-details details-overlay details-reset width-full"> - <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block"> - Explore - <svg x="0px" y="0px" viewBox="0 0 14 8" xml:space="preserve" fill="none" class="icon-chevon-down-mktg position-absolute position-lg-relative"> - <path d="M1,1l6.2,6L13,1"></path> - </svg> - </summary> - - <div class="dropdown-menu flex-auto rounded-1 bg-white px-0 pt-2 pb-0 mt-0 pb-4 p-lg-4 position-relative position-lg-absolute left-0 left-lg-n4"> - <ul class="list-style-none mb-3"> - <li class="edge-item-fix"><a href="/explore" class="py-2 lh-condensed-ultra d-block link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Explore">Explore GitHub <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a></li> - </ul> - - <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Learn & contribute</h4> - <ul class="list-style-none mb-3"> - <li class="edge-item-fix"><a href="/topics" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Topics">Topics</a></li> - <li class="edge-item-fix"><a href="/collections" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Collections">Collections</a></li> - <li class="edge-item-fix"><a href="/trending" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Trending">Trending</a></li> - <li class="edge-item-fix"><a href="https://lab.github.com/" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Learning lab">Learning Lab</a></li> - <li class="edge-item-fix"><a href="https://opensource.guide" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Open source guides">Open source guides</a></li> - </ul> - - <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Connect with others</h4> - <ul class="list-style-none mb-0"> - <li class="edge-item-fix"><a href="https://github.com/events" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Events">Events</a></li> - <li class="edge-item-fix"><a href="https://github.community" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Community forum">Community forum</a></li> - <li class="edge-item-fix"><a href="https://education.github.com" class="py-2 pb-0 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to GitHub Education">GitHub Education</a></li> - </ul> - </div> - </details> - </li> - - <li class="border-bottom border-lg-bottom-0 mr-0 mr-lg-3"> - <a href="/marketplace" class="HeaderMenu-link no-underline py-3 d-block d-lg-inline-block" data-ga-click="(Logged out) Header, go to Marketplace">Marketplace</a> - </li> - - <li class="d-block d-lg-flex flex-lg-nowrap flex-lg-items-center border-bottom border-lg-bottom-0 mr-0 mr-lg-3 edge-item-fix position-relative flex-wrap flex-justify-between d-flex flex-items-center "> - <details class="HeaderMenu-details details-overlay details-reset width-full"> - <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block"> - Pricing - <svg x="0px" y="0px" viewBox="0 0 14 8" xml:space="preserve" fill="none" class="icon-chevon-down-mktg position-absolute position-lg-relative"> - <path d="M1,1l6.2,6L13,1"></path> - </svg> - </summary> - - <div class="dropdown-menu flex-auto rounded-1 bg-white px-0 pt-2 pb-4 mt-0 p-lg-4 position-relative position-lg-absolute left-0 left-lg-n4"> - <a href="/pricing" class="pb-2 lh-condensed-ultra d-block link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Pricing">Plans <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a> - - <ul class="list-style-none mb-3"> - <li class="edge-item-fix"><a href="/pricing#feature-comparison" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Compare plans">Compare plans</a></li> - <li class="edge-item-fix"><a href="https://enterprise.github.com/contact" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Contact Sales">Contact Sales</a></li> - </ul> - - <ul class="list-style-none mb-0 border-lg-top pt-lg-3"> - <li class="edge-item-fix"><a href="/nonprofit" class="py-2 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Nonprofits">Nonprofit <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a></li> - <li class="edge-item-fix"><a href="https://education.github.com" class="py-2 pb-0 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Education">Education <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a></li> - </ul> - </div> - </details> - </li> - </ul> - </nav> - - <div class="d-lg-flex flex-items-center px-3 px-lg-0 text-center text-lg-left"> - <div class="d-lg-flex mb-3 mb-lg-0"> - <div class="header-search flex-self-stretch flex-lg-self-auto mr-0 mr-lg-3 mb-3 mb-lg-0 scoped-search site-scoped-search js-site-search position-relative js-jump-to" - role="combobox" - aria-owns="jump-to-results" - aria-label="Search or jump to" - aria-haspopup="listbox" - aria-expanded="false" -> - <div class="position-relative"> - <!-- '"` --><!-- </textarea></xmp> --></option></form><form class="js-site-search-form" role="search" aria-label="Site" data-scope-type="Repository" data-scope-id="139730674" data-scoped-search-url="/johnheap/VAPPER-Galaxy/search" data-unscoped-search-url="/search" action="/johnheap/VAPPER-Galaxy/search" accept-charset="UTF-8" method="get"><input name="utf8" type="hidden" value="✓" /> - <label class="form-control input-sm header-search-wrapper p-0 header-search-wrapper-jump-to position-relative d-flex flex-justify-between flex-items-center js-chromeless-input-container"> - <input type="text" - class="form-control input-sm header-search-input jump-to-field js-jump-to-field js-site-search-focus js-site-search-field is-clearable" - data-hotkey="s,/" - name="q" - value="" - placeholder="Search" - data-unscoped-placeholder="Search GitHub" - data-scoped-placeholder="Search" - autocapitalize="off" - aria-autocomplete="list" - aria-controls="jump-to-results" - aria-label="Search" - data-jump-to-suggestions-path="/_graphql/GetSuggestedNavigationDestinations#csrf-token=LLJ+OkKE/IZSGE41x4AcvzTEKCr0Qf3xRwqCk3aGbTfPUFI4bEfVJMEjdi/KtSrGkaRXbzT9uHf76IjFxxMf2w==" - spellcheck="false" - autocomplete="off" - > - <input type="hidden" class="js-site-search-type-field" name="type" > - <img src="https://github.githubassets.com/images/search-key-slash.svg" alt="" class="mr-2 header-search-key-slash"> - - <div class="Box position-absolute overflow-hidden d-none jump-to-suggestions js-jump-to-suggestions-container"> - -<ul class="d-none js-jump-to-suggestions-template-container"> - - -<li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-suggestion" role="option"> - <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href=""> - <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> - <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> - <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg> - <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg> - </div> - - <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> - - <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> - </div> - - <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search"> - <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> - In this repository - </span> - <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> - All GitHub - </span> - <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> - </div> - - <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> - Jump to - <span class="d-inline-block ml-1 v-align-middle">↵</span> - </div> - </a> -</li> - -</ul> - -<ul class="d-none js-jump-to-no-results-template-container"> - <li class="d-flex flex-justify-center flex-items-center f5 d-none js-jump-to-suggestion p-2"> - <span class="text-gray">No suggested jump to results</span> - </li> -</ul> - -<ul id="jump-to-results" role="listbox" class="p-0 m-0 js-navigation-container jump-to-suggestions-results-container js-jump-to-suggestions-results-container"> - - -<li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-scoped-search d-none" role="option"> - <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href=""> - <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> - <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> - <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg> - <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg> - </div> - - <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> - - <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> - </div> - - <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search"> - <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> - In this repository - </span> - <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> - All GitHub - </span> - <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> - </div> - - <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> - Jump to - <span class="d-inline-block ml-1 v-align-middle">↵</span> - </div> - </a> -</li> - - - -<li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-global-search d-none" role="option"> - <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href=""> - <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> - <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> - <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg> - <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg> - </div> - - <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> - - <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> - </div> - - <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search"> - <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> - In this repository - </span> - <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> - All GitHub - </span> - <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> - </div> - - <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> - Jump to - <span class="d-inline-block ml-1 v-align-middle">↵</span> - </div> - </a> -</li> - - -</ul> - - </div> - </label> -</form> </div> -</div> - - </div> - - <a class="HeaderMenu-link no-underline mr-3" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header menu","repository_id":null,"auth_type":"LOG_IN","client_id":null,"originating_request_id":"A685:3C8B:6E284:CA64B:5CF5611F","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/README.md","referrer":null,"user_id":null}}" data-hydro-click-hmac="ebd8ffd02f6a18636a4b072c4046f415890307024977cd4253078df3834ed8da" data-ga-click="(Logged out) Header, clicked Sign in, text:sign-in" href="/login?return_to=%2Fjohnheap%2FVAPPER-Galaxy%2Fblob%2Fmaster%2FREADME.md"> - Sign in -</a> <a class="HeaderMenu-link d-inline-block no-underline border border-gray-dark rounded-1 px-2 py-1" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header menu","repository_id":null,"auth_type":"SIGN_UP","client_id":null,"originating_request_id":"A685:3C8B:6E284:CA64B:5CF5611F","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/README.md","referrer":null,"user_id":null}}" data-hydro-click-hmac="8e547045a6e3dc5ede127bb41fa3aca2fb5dd4abb49a24821780724608ad1b76" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up" href="/join?source=header-repo"> - Sign up -</a> </div> - </div> - </div> -</header> - - </div> - - <div id="start-of-content" class="show-on-focus"></div> - - - <div id="js-flash-container"> - -</div> - - - - <div class="application-main " data-commit-hovercards-enabled> - <div itemscope itemtype="http://schema.org/SoftwareSourceCode" class=""> - <main > - - - - - - - - - - - <div class="pagehead repohead instapaper_ignore readability-menu experiment-repo-nav pt-0 pt-lg-4 "> - <div class="repohead-details-container clearfix container-lg p-responsive d-none d-lg-block"> - - <ul class="pagehead-actions"> - - - - - <li> - - <a class="tooltipped tooltipped-s btn btn-sm btn-with-count" aria-label="You must be signed in to watch a repository" rel="nofollow" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"notification subscription menu watch","repository_id":null,"auth_type":"LOG_IN","client_id":null,"originating_request_id":"A685:3C8B:6E284:CA64B:5CF5611F","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/README.md","referrer":null,"user_id":null}}" data-hydro-click-hmac="f3eddf81a891abbd0e93ec9a1f96d7bf9399a35fc143a76c162db9833f530563" href="/login?return_to=%2Fjohnheap%2FVAPPER-Galaxy"> - <svg class="octicon octicon-eye v-align-text-bottom" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.06 2C3 2 0 8 0 8s3 6 8.06 6C13 14 16 8 16 8s-3-6-7.94-6zM8 12c-2.2 0-4-1.78-4-4 0-2.2 1.8-4 4-4 2.22 0 4 1.8 4 4 0 2.22-1.78 4-4 4zm2-4c0 1.11-.89 2-2 2-1.11 0-2-.89-2-2 0-1.11.89-2 2-2 1.11 0 2 .89 2 2z"/></svg> - Watch -</a> <a class="social-count" href="/johnheap/VAPPER-Galaxy/watchers" - aria-label="0 users are watching this repository"> - 0 - </a> - - </li> - - <li> - <a class="btn btn-sm btn-with-count tooltipped tooltipped-s" aria-label="You must be signed in to star a repository" rel="nofollow" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"star button","repository_id":139730674,"auth_type":"LOG_IN","client_id":null,"originating_request_id":"A685:3C8B:6E284:CA64B:5CF5611F","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/README.md","referrer":null,"user_id":null}}" data-hydro-click-hmac="db5d83edbb555863a80874af492285a40e1560b7ced90b5d20a48bbca018c19f" href="/login?return_to=%2Fjohnheap%2FVAPPER-Galaxy"> - <svg class="octicon octicon-star v-align-text-bottom" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M14 6l-4.9-.64L7 1 4.9 5.36 0 6l3.6 3.26L2.67 14 7 11.67 11.33 14l-.93-4.74L14 6z"/></svg> - Star -</a> - <a class="social-count js-social-count" href="/johnheap/VAPPER-Galaxy/stargazers" - aria-label="0 users starred this repository"> - 0 - </a> - - </li> - - <li> - <a class="btn btn-sm btn-with-count tooltipped tooltipped-s" aria-label="You must be signed in to fork a repository" rel="nofollow" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"repo details fork button","repository_id":139730674,"auth_type":"LOG_IN","client_id":null,"originating_request_id":"A685:3C8B:6E284:CA64B:5CF5611F","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/README.md","referrer":null,"user_id":null}}" data-hydro-click-hmac="84c6fc6927ea6fbb4c3f083249472989e34d4b9c5c7f82eb78b5657dc0046cdf" href="/login?return_to=%2Fjohnheap%2FVAPPER-Galaxy"> - <svg class="octicon octicon-repo-forked v-align-text-bottom" viewBox="0 0 10 16" version="1.1" width="10" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8 1a1.993 1.993 0 0 0-1 3.72V6L5 8 3 6V4.72A1.993 1.993 0 0 0 2 1a1.993 1.993 0 0 0-1 3.72V6.5l3 3v1.78A1.993 1.993 0 0 0 5 15a1.993 1.993 0 0 0 1-3.72V9.5l3-3V4.72A1.993 1.993 0 0 0 8 1zM2 4.2C1.34 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm3 10c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm3-10c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg> - Fork -</a> - <a href="/johnheap/VAPPER-Galaxy/network/members" class="social-count" - aria-label="0 users forked this repository"> - 0 - </a> - </li> -</ul> - - <h1 class="public "> - <svg class="octicon octicon-repo" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> - <span class="author" itemprop="author"><a class="url fn" rel="author" data-hovercard-type="user" data-hovercard-url="/hovercards?user_id=24318980" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/johnheap">johnheap</a></span><!-- ---><span class="path-divider">/</span><!-- ---><strong itemprop="name"><a data-pjax="#js-repo-pjax-container" href="/johnheap/VAPPER-Galaxy">VAPPER-Galaxy</a></strong> - - -</h1> - - </div> - -<nav class="hx_reponav reponav js-repo-nav js-sidenav-container-pjax container-lg p-responsive d-none d-lg-block" - itemscope - itemtype="http://schema.org/BreadcrumbList" - aria-label="Repository" - data-pjax="#js-repo-pjax-container"> - - <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement"> - <a class="js-selected-navigation-item selected reponav-item" itemprop="url" data-hotkey="g c" aria-current="page" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches repo_packages /johnheap/VAPPER-Galaxy" href="/johnheap/VAPPER-Galaxy"> - <svg class="octicon octicon-code" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M9.5 3L8 4.5 11.5 8 8 11.5 9.5 13 14 8 9.5 3zm-5 0L0 8l4.5 5L6 11.5 2.5 8 6 4.5 4.5 3z"/></svg> - <span itemprop="name">Code</span> - <meta itemprop="position" content="1"> -</a> </span> - - <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement"> - <a itemprop="url" data-hotkey="g i" class="js-selected-navigation-item reponav-item" data-selected-links="repo_issues repo_labels repo_milestones /johnheap/VAPPER-Galaxy/issues" href="/johnheap/VAPPER-Galaxy/issues"> - <svg class="octicon octicon-issue-opened" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7 2.3c3.14 0 5.7 2.56 5.7 5.7s-2.56 5.7-5.7 5.7A5.71 5.71 0 0 1 1.3 8c0-3.14 2.56-5.7 5.7-5.7zM7 1C3.14 1 0 4.14 0 8s3.14 7 7 7 7-3.14 7-7-3.14-7-7-7zm1 3H6v5h2V4zm0 6H6v2h2v-2z"/></svg> - <span itemprop="name">Issues</span> - <span class="Counter">0</span> - <meta itemprop="position" content="2"> -</a> </span> - - <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement"> - <a data-hotkey="g p" itemprop="url" class="js-selected-navigation-item reponav-item" data-selected-links="repo_pulls checks /johnheap/VAPPER-Galaxy/pulls" href="/johnheap/VAPPER-Galaxy/pulls"> - <svg class="octicon octicon-git-pull-request" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M11 11.28V5c-.03-.78-.34-1.47-.94-2.06C9.46 2.35 8.78 2.03 8 2H7V0L4 3l3 3V4h1c.27.02.48.11.69.31.21.2.3.42.31.69v6.28A1.993 1.993 0 0 0 10 15a1.993 1.993 0 0 0 1-3.72zm-1 2.92c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zM4 3c0-1.11-.89-2-2-2a1.993 1.993 0 0 0-1 3.72v6.56A1.993 1.993 0 0 0 2 15a1.993 1.993 0 0 0 1-3.72V4.72c.59-.34 1-.98 1-1.72zm-.8 10c0 .66-.55 1.2-1.2 1.2-.65 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2zM2 4.2C1.34 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg> - <span itemprop="name">Pull requests</span> - <span class="Counter">0</span> - <meta itemprop="position" content="3"> -</a> </span> - - - <a data-hotkey="g b" class="js-selected-navigation-item reponav-item" data-selected-links="repo_projects new_repo_project repo_project /johnheap/VAPPER-Galaxy/projects" href="/johnheap/VAPPER-Galaxy/projects"> - <svg class="octicon octicon-project" viewBox="0 0 15 16" version="1.1" width="15" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg> - Projects - <span class="Counter" >0</span> -</a> - - - <a data-skip-pjax="true" class="js-selected-navigation-item reponav-item" data-selected-links="security alerts policy /johnheap/VAPPER-Galaxy/security/advisories" href="/johnheap/VAPPER-Galaxy/security/advisories"> - <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 16 16" class="octicon" height="16px" width="16px"> - <path fill-rule="evenodd" clip-rule="evenodd" d="M1 2l7-2 7 2v6.02C15 12.69 9.69 16 8 16c-1.69 0-7-3.31-7-7.98V2zm1 .75L8 1l6 1.75v5.268C14 12.104 9.45 15 8 15c-1.45 0-6-2.896-6-6.982V2.75z"></path> - <path d="M3 3.5L8 2v12c-1.207 0-5-2.482-5-5.985V3.5z"></path> -</svg> - - Security -</a> - <a class="js-selected-navigation-item reponav-item" data-selected-links="repo_graphs repo_contributors dependency_graph pulse people /johnheap/VAPPER-Galaxy/pulse" href="/johnheap/VAPPER-Galaxy/pulse"> - <svg class="octicon octicon-graph" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M16 14v1H0V0h1v14h15zM5 13H3V8h2v5zm4 0H7V3h2v10zm4 0h-2V6h2v7z"/></svg> - Insights -</a> - -</nav> - - <div class="reponav-wrapper reponav-small d-lg-none"> - <nav class="reponav js-reponav text-center no-wrap" - itemscope - itemtype="http://schema.org/BreadcrumbList"> - - <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement"> - <a class="js-selected-navigation-item selected reponav-item" itemprop="url" aria-current="page" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches repo_packages /johnheap/VAPPER-Galaxy" href="/johnheap/VAPPER-Galaxy"> - <span itemprop="name">Code</span> - <meta itemprop="position" content="1"> -</a> </span> - - <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement"> - <a itemprop="url" class="js-selected-navigation-item reponav-item" data-selected-links="repo_issues repo_labels repo_milestones /johnheap/VAPPER-Galaxy/issues" href="/johnheap/VAPPER-Galaxy/issues"> - <span itemprop="name">Issues</span> - <span class="Counter">0</span> - <meta itemprop="position" content="2"> -</a> </span> - - <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement"> - <a itemprop="url" class="js-selected-navigation-item reponav-item" data-selected-links="repo_pulls checks /johnheap/VAPPER-Galaxy/pulls" href="/johnheap/VAPPER-Galaxy/pulls"> - <span itemprop="name">Pull requests</span> - <span class="Counter">0</span> - <meta itemprop="position" content="3"> -</a> </span> - - <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement"> - <a itemprop="url" class="js-selected-navigation-item reponav-item" data-selected-links="repo_projects new_repo_project repo_project /johnheap/VAPPER-Galaxy/projects" href="/johnheap/VAPPER-Galaxy/projects"> - <span itemprop="name">Projects</span> - <span class="Counter">0</span> - <meta itemprop="position" content="4"> -</a> </span> - - - <a itemprop="url" class="js-selected-navigation-item reponav-item" data-selected-links="security alerts policy /johnheap/VAPPER-Galaxy/security/advisories" href="/johnheap/VAPPER-Galaxy/security/advisories"> - <span itemprop="name">Security</span> - <meta itemprop="position" content="6"> -</a> - <a class="js-selected-navigation-item reponav-item" data-selected-links="pulse /johnheap/VAPPER-Galaxy/pulse" href="/johnheap/VAPPER-Galaxy/pulse"> - Pulse -</a> - - </nav> -</div> - - - </div> -<div class="container-lg new-discussion-timeline experiment-repo-nav p-responsive"> - <div class="repository-content "> - - - - - - - - <a class="d-none js-permalink-shortcut" data-hotkey="y" href="/johnheap/VAPPER-Galaxy/blob/a4e16d71fe985f389930c02f94354b87d3aabadb/README.md">Permalink</a> - - <!-- blob contrib key: blob_contributors:v21:9b9749a0cb47d58fdd9deb496d862ff4 --> - <div class="signup-prompt-bg rounded-1"> - <div class="signup-prompt p-4 text-center mb-4 rounded-1"> - <div class="position-relative"> - <!-- '"` --><!-- </textarea></xmp> --></option></form><form action="/prompt_dismissals/signup" accept-charset="UTF-8" method="post"><input name="utf8" type="hidden" value="✓" /><input type="hidden" name="_method" value="put" /><input type="hidden" name="authenticity_token" value="RiQSoI9sdJfGg2XsgayNBNfrGAanADzW1sdx6maKwXz2R08zS2nf5z5o4XlSxZVvdTmOC4vvjVFMFT0S3rlsPw==" /> - <button type="submit" class="position-absolute top-0 right-0 btn-link link-gray" data-ga-click="(Logged out) Sign up prompt, clicked Dismiss, text:dismiss"> - Dismiss - </button> -</form> <h3 class="pt-2">Join GitHub today</h3> - <p class="col-6 mx-auto">GitHub is home to over 36 million developers working together to host and review code, manage projects, and build software together.</p> - <a class="btn btn-primary" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"files signup prompt","repository_id":null,"auth_type":"SIGN_UP","client_id":null,"originating_request_id":"A685:3C8B:6E284:CA64B:5CF5611F","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/README.md","referrer":null,"user_id":null}}" data-hydro-click-hmac="4da02a6c5b2e5c9e08052d3d23deb4bc99ea4f093f010a9b5cec6320bd7b0dba" data-ga-click="(Logged out) Sign up prompt, clicked Sign up, text:sign-up" href="/join?source=prompt-blob-show">Sign up</a> - </div> - </div> - </div> - - - <div class="d-flex flex-items-start flex-shrink-0 mb-2 flex-column flex-md-row"> - <span class="d-flex flex-justify-between width-full width-md-auto"> - -<details class="details-reset details-overlay select-menu branch-select-menu hx_rsm" id="branch-select-menu"> - <summary class="btn btn-sm select-menu-button css-truncate" - data-hotkey="w" - - title="Switch branches or tags"> - <i>Branch:</i> - <span class="css-truncate-target">master</span> - </summary> - - <details-menu class="select-menu-modal hx_rsm-modal position-absolute" style="z-index: 99;" src="/johnheap/VAPPER-Galaxy/ref-list/master/README.md?source_action=show&source_controller=blob" preload> - <include-fragment class="select-menu-loading-overlay anim-pulse"> - <svg height="32" class="octicon octicon-octoface" viewBox="0 0 16 16" version="1.1" width="32" aria-hidden="true"><path fill-rule="evenodd" d="M14.7 5.34c.13-.32.55-1.59-.13-3.31 0 0-1.05-.33-3.44 1.3-1-.28-2.07-.32-3.13-.32s-2.13.04-3.13.32c-2.39-1.64-3.44-1.3-3.44-1.3-.68 1.72-.26 2.99-.13 3.31C.49 6.21 0 7.33 0 8.69 0 13.84 3.33 15 7.98 15S16 13.84 16 8.69c0-1.36-.49-2.48-1.3-3.35zM8 14.02c-3.3 0-5.98-.15-5.98-3.35 0-.76.38-1.48 1.02-2.07 1.07-.98 2.9-.46 4.96-.46 2.07 0 3.88-.52 4.96.46.65.59 1.02 1.3 1.02 2.07 0 3.19-2.68 3.35-5.98 3.35zM5.49 9.01c-.66 0-1.2.8-1.2 1.78s.54 1.79 1.2 1.79c.66 0 1.2-.8 1.2-1.79s-.54-1.78-1.2-1.78zm5.02 0c-.66 0-1.2.79-1.2 1.78s.54 1.79 1.2 1.79c.66 0 1.2-.8 1.2-1.79s-.53-1.78-1.2-1.78z"/></svg> - </include-fragment> - </details-menu> -</details> - - <div class="BtnGroup flex-shrink-0 d-md-none"> - <a href="/johnheap/VAPPER-Galaxy/find/master" - class="js-pjax-capture-input btn btn-sm BtnGroup-item" - data-pjax - data-hotkey="t"> - Find file - </a> - <clipboard-copy value="README.md" class="btn btn-sm BtnGroup-item"> - Copy path - </clipboard-copy> - </div> - </span> - <h2 id="blob-path" class="breadcrumb flex-auto min-width-0 text-normal flex-md-self-center ml-md-2 mr-md-3 my-2 my-md-0"> - <span class="js-repo-root text-bold"><span class="js-path-segment"><a data-pjax="true" href="/johnheap/VAPPER-Galaxy"><span>VAPPER-Galaxy</span></a></span></span><span class="separator">/</span><strong class="final-path">README.md</strong> - </h2> - - <div class="BtnGroup flex-shrink-0 d-none d-md-inline-block"> - <a href="/johnheap/VAPPER-Galaxy/find/master" - class="js-pjax-capture-input btn btn-sm BtnGroup-item" - data-pjax - data-hotkey="t"> - Find file - </a> - <clipboard-copy value="README.md" class="btn btn-sm BtnGroup-item"> - Copy path - </clipboard-copy> - </div> - </div> - - - - <include-fragment src="/johnheap/VAPPER-Galaxy/contributors/master/README.md" class="Box Box--condensed commit-loader"> - <div class="Box-body bg-blue-light f6"> - Fetching contributors… - </div> - - <div class="Box-body d-flex flex-items-center" > - <img alt="" class="loader-loading mr-2" src="https://github.githubassets.com/images/spinners/octocat-spinner-32-EAF2F5.gif" width="16" height="16" /> - <span class="text-red h6 loader-error">Cannot retrieve contributors at this time</span> - </div> -</include-fragment> - - - - - - <div class="Box mt-3 position-relative"> - -<div class="Box-header py-2 d-flex flex-column flex-shrink-0 flex-md-row flex-md-items-center"> - - <div class="text-mono f6 flex-auto pr-3 flex-order-2 flex-md-order-1 mt-2 mt-md-0"> - 25 lines (13 sloc) - <span class="file-info-divider"></span> - 2.52 KB - </div> - - <div class="d-flex py-1 py-md-0 flex-auto flex-order-1 flex-md-order-2 flex-sm-grow-0 flex-justify-between"> - - <div class="BtnGroup"> - <a id="raw-url" class="btn btn-sm BtnGroup-item" href="/johnheap/VAPPER-Galaxy/raw/master/README.md">Raw</a> - <a class="btn btn-sm js-update-url-with-hash BtnGroup-item" data-hotkey="b" href="/johnheap/VAPPER-Galaxy/blame/master/README.md">Blame</a> - <a rel="nofollow" class="btn btn-sm BtnGroup-item" href="/johnheap/VAPPER-Galaxy/commits/master/README.md">History</a> - </div> - - - <div> - - <button type="button" class="btn-octicon disabled tooltipped tooltipped-nw" - aria-label="You must be signed in to make or propose changes"> - <svg class="octicon octicon-pencil" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M0 12v3h3l8-8-3-3-8 8zm3 2H1v-2h1v1h1v1zm10.3-9.3L12 6 9 3l1.3-1.3a.996.996 0 0 1 1.41 0l1.59 1.59c.39.39.39 1.02 0 1.41z"/></svg> - </button> - <button type="button" class="btn-octicon btn-octicon-danger disabled tooltipped tooltipped-nw" - aria-label="You must be signed in to make or propose changes"> - <svg class="octicon octicon-trashcan" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M11 2H9c0-.55-.45-1-1-1H5c-.55 0-1 .45-1 1H2c-.55 0-1 .45-1 1v1c0 .55.45 1 1 1v9c0 .55.45 1 1 1h7c.55 0 1-.45 1-1V5c.55 0 1-.45 1-1V3c0-.55-.45-1-1-1zm-1 12H3V5h1v8h1V5h1v8h1V5h1v8h1V5h1v9zm1-10H2V3h9v1z"/></svg> - </button> - </div> - </div> -</div> - - - <div id="readme" class="Box-body readme blob instapaper_body js-code-block-container"> - <article class="markdown-body entry-content p-3 p-md-6" itemprop="text"><p>This is the repository associated with the VAPPER Galaxy Tool available in the Galaxy Toolshed -VAPP accurately quantifies the variant antigen diversity in Trypanosoma congolense isolates or the variable Cog presence in T.vivax isolates</p> -<p>The Trypanosoma congolense variant antigen repertoire is divided into 15 clades or phylotypes. These phylotypes are present in any T. congolense isolate, but their relative abundance varies between strains. The purpose of the VAPPER is to accurately quantify antigen diversity in any T. congolense isolate by calculating the relative frequency of each phylotype.</p> -<p>The Galaxy VAPPER Tool has four modes.</p> -<ol> -<li> -<p>T.congolense Genomic: -This takes raw NGS reads (or pre-assmebled contigs) as input, assembles them de-novo, searches for evidence of each phylotype based on hidden Markov models (HMM), and calculates their relative abundances. -The results are visualized in three different ways: a table with each phylotype and their relative frequencies as proportions of the full repertoire in the given genome; a heat map with dendogram showing either absolute VAP variation or deviation from the mean, using our pilot dataset; and a Principal Component Analysis (PCA) plot showing variation distribution in the given sample compared to our pilot dataset.</p> -</li> -<li> -<p>T.congolense Transcriptomic: -This requires NGS paired reads and uses bowtie2 and samtools for read mapping and processing, cufflinks for transcript abundance estimation, and hmmer for sequence identification. The output is a stacked bar chart and a table of frequencies based on the transcript abundances.</p> -</li> -<li> -<p>T.vivax clusters of orthologs -The approach for T. vivax relies on the presence/absence of clusters of orthologs (COGs). It requires velvet for the genome assembly and blast. it recieves paired sequencing reads in fastq format (or a contig file if already assembled) and the output is a binary matrix of the presence/absence of each COG/gene for a given sample. Within the tool there is a database of 28 isolates that are used as a comparison producing a heatmap and dendogram.</p> -</li> -<li> -<p>T.vivax Transcriptomic pathway -This method takes two NGS paired reads, maps the transcripts against a user supplied reference file and then estimates the trancript aboundance (using samtools and cufflinks). The output is then binned into 175 predefined phylotypes based on their greatest blastx similarity (this table is available in the results directory). A pident of less than 70% is considered unidentified. The results provide a tabular and graphical phylotype profile of the sample(s)</p> -</li> -</ol> -</article> - </div> - - </div> - - - - <details class="details-reset details-overlay details-overlay-dark"> - <summary data-hotkey="l" aria-label="Jump to line"></summary> - <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast linejump" aria-label="Jump to line"> - <!-- '"` --><!-- </textarea></xmp> --></option></form><form class="js-jump-to-line-form Box-body d-flex" action="" accept-charset="UTF-8" method="get"><input name="utf8" type="hidden" value="✓" /> - <input class="form-control flex-auto mr-3 linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" aria-label="Jump to line" autofocus> - <button type="submit" class="btn" data-close-dialog>Go</button> -</form> </details-dialog> - </details> - - - - </div> - <div class="modal-backdrop js-touch-events"></div> -</div> - - </main> - </div> - - - </div> - - -<div class="footer container-lg width-full p-responsive" role="contentinfo"> - <div class="position-relative d-flex flex-row-reverse flex-lg-row flex-wrap flex-lg-nowrap flex-justify-center flex-lg-justify-between pt-6 pb-2 mt-6 f6 text-gray border-top border-gray-light "> - <ul class="list-style-none d-flex flex-wrap col-12 col-lg-5 flex-justify-center flex-lg-justify-between mb-2 mb-lg-0"> - <li class="mr-3 mr-lg-0">© 2019 <span title="0.30328s from unicorn-74746df85b-4dkrb">GitHub</span>, Inc.</li> - <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to terms, text:terms" href="https://github.com/site/terms">Terms</a></li> - <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to privacy, text:privacy" href="https://github.com/site/privacy">Privacy</a></li> - <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to security, text:security" href="https://github.com/security">Security</a></li> - <li class="mr-3 mr-lg-0"><a href="https://githubstatus.com/" data-ga-click="Footer, go to status, text:status">Status</a></li> - <li><a data-ga-click="Footer, go to help, text:help" href="https://help.github.com">Help</a></li> - </ul> - - <a aria-label="Homepage" title="GitHub" class="footer-octicon d-none d-lg-block mx-lg-4" href="https://github.com"> - <svg height="24" class="octicon octicon-mark-github" viewBox="0 0 16 16" version="1.1" width="24" aria-hidden="true"><path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"/></svg> -</a> - <ul class="list-style-none d-flex flex-wrap col-12 col-lg-5 flex-justify-center flex-lg-justify-between mb-2 mb-lg-0"> - <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to contact, text:contact" href="https://github.com/contact">Contact GitHub</a></li> - <li class="mr-3 mr-lg-0"><a href="https://github.com/pricing" data-ga-click="Footer, go to Pricing, text:Pricing">Pricing</a></li> - <li class="mr-3 mr-lg-0"><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li> - <li class="mr-3 mr-lg-0"><a href="https://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li> - <li class="mr-3 mr-lg-0"><a href="https://github.blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li> - <li><a data-ga-click="Footer, go to about, text:about" href="https://github.com/about">About</a></li> - - </ul> - </div> - <div class="d-flex flex-justify-center pb-6"> - <span class="f6 text-gray-light"></span> - </div> -</div> - - - - <div id="ajax-error-message" class="ajax-error-message flash flash-error"> - <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg> - <button type="button" class="flash-close js-ajax-error-dismiss" aria-label="Dismiss error"> - <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg> - </button> - You can’t perform that action at this time. - </div> - - - <script crossorigin="anonymous" integrity="sha512-EPrD+nddbyhpiLL8l3M8VfJpZr4J2EWQLaPXZ+6A3VDJKzS5HeZ3dkMVieHSdvIPHsMbWPyVlY42SWKoS4XTfA==" type="application/javascript" src="https://github.githubassets.com/assets/compat-bootstrap-831f12d4.js"></script> - <script crossorigin="anonymous" integrity="sha512-oFBEYscCdWEyvUQehaYyaCSiKtIN4UvpfFHNpIXLUTSQ35JcacPNj86R8fgJfI1e7BOjbLZPTv1nJg3TECiMLw==" type="application/javascript" src="https://github.githubassets.com/assets/frameworks-7af24171.js"></script> - - <script crossorigin="anonymous" async="async" integrity="sha512-b9BDH7EZq1yaR2fUH08I378zVkToScLiQ//L0gdyPviliuwpWiVFkB8uW0K8zZszdeLeBpib7wGBLkPiIFgyHg==" type="application/javascript" src="https://github.githubassets.com/assets/github-bootstrap-2a8c2b54.js"></script> - - - - <div class="js-stale-session-flash stale-session-flash flash flash-warn flash-banner" hidden - > - <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg> - <span class="signed-in-tab-flash">You signed in with another tab or window. <a href="">Reload</a> to refresh your session.</span> - <span class="signed-out-tab-flash">You signed out in another tab or window. <a href="">Reload</a> to refresh your session.</span> - </div> - <template id="site-details-dialog"> - <details class="details-reset details-overlay details-overlay-dark lh-default text-gray-dark hx_rsm" open> - <summary role="button" aria-label="Close dialog"></summary> - <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast hx_rsm-dialog hx_rsm-modal"> - <button class="Box-btn-octicon m-0 btn-octicon position-absolute right-0 top-0" type="button" aria-label="Close dialog" data-close-dialog> - <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg> - </button> - <div class="octocat-spinner my-6 js-details-dialog-spinner"></div> - </details-dialog> - </details> -</template> - - <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;" tabindex="0"> - <div class="Popover-message Popover-message--bottom-left Popover-message--large Box box-shadow-large" style="width:360px;"> - </div> -</div> - - <div aria-live="polite" class="js-global-screen-reader-notice sr-only"></div> - - </body> -</html> -