fixed vgraph git clone

MRCIEU · Mar 29, 2022 · d1e9f9d · d1e9f9d
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diff --git a/Dockerfile b/Dockerfile
@@ -9,7 +9,7 @@ WORKDIR /app
 # install python dependencies
 RUN pip install --upgrade pip
 RUN pip install -r requirements.txt
-RUN pip install git+git://github.com/bioinformed/[email protected]#egg=vgraph
+RUN pip install git+https://github.com/bioinformed/[email protected]#egg=vgraph
 
 # launch app
 CMD ["python", "main.py"]
diff --git a/docs/404.html b/docs/404.html
@@ -1,90 +1,76 @@
 <!DOCTYPE html>
-<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
-<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<html class="writer-html5" lang="en" >
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-  <meta charset="utf-8">
-  <meta http-equiv="X-UA-Compatible" content="IE=edge">
-  <meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-
-
-  <link rel="shortcut icon" href="/gwas2vcf/img/favicon.ico">
-  <title>gwas2vcf</title>
-  <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Lato:400,700|Roboto+Slab:400,700|Inconsolata:400,700" />
-
-  <link rel="stylesheet" href="/gwas2vcf/css/theme.css" />
-  <link rel="stylesheet" href="/gwas2vcf/css/theme_extra.css" />
-  <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/10.5.0/styles/github.min.css" />
-
-  <script src="/gwas2vcf/js/jquery-2.1.1.min.js" defer></script>
-  <script src="/gwas2vcf/js/modernizr-2.8.3.min.js" defer></script>
-  <script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/10.5.0/highlight.min.js"></script>
-  <script>hljs.initHighlightingOnLoad();</script> 
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+      <link rel="shortcut icon" href="/gwas2vcf/img/favicon.ico" />
+    <title>gwas2vcf</title>
+    <link rel="stylesheet" href="/gwas2vcf/css/theme.css" />
+    <link rel="stylesheet" href="/gwas2vcf/css/theme_extra.css" />
+        <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/10.5.0/styles/github.min.css" />
+
+    <script src="/gwas2vcf/js/jquery-3.6.0.min.js" defer></script>
+    <!--[if lt IE 9]>
+      <script src="/gwas2vcf/js/html5shiv.min.js"></script>
+    <![endif]-->
+      <script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/10.5.0/highlight.min.js"></script>
+      <script>hljs.initHighlightingOnLoad();</script> 
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+          <a href="/gwas2vcf/." class="icon icon-home"> gwas2vcf
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-                <ul>
-                    <li class="toctree-l1"><a class="reference internal" href="/gwas2vcf/downstream/">Downstream analyses</a>
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+      <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <ul>
+                <li class="toctree-l1"><a class="reference internal" href="/gwas2vcf/.">Home</a>
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+              <ul>
+                <li class="toctree-l1"><a class="reference internal" href="/gwas2vcf/install/">Install</a>
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+              </ul>
+              <ul>
+                <li class="toctree-l1"><a class="reference internal" href="/gwas2vcf/tutorial/">Tutorial</a>
+                </li>
+              </ul>
+              <ul>
+                <li class="toctree-l1"><a class="reference internal" href="/gwas2vcf/downstream/">Downstream analyses</a>
+                </li>
+              </ul>
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+        <div class="rst-content"><div role="navigation" aria-label="breadcrumbs navigation">
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-    <li><a href="/gwas2vcf/.">Docs</a> &raquo;</li>
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+    <li><a href="/gwas2vcf/." class="icon icon-home" alt="Docs"></a> &raquo;</li>
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+            <div class="section" itemprop="articleBody">
 
 
   <h1 id="404-page-not-found">404</h1>
@@ -93,28 +79,25 @@ <h1 id="404-page-not-found">404</h1>
 
 
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diff --git a/...fonts/RobotoSlab/roboto-slab-v7-bold.woff → docs/css/fonts/Roboto-Slab-Bold.woff b/...fonts/RobotoSlab/roboto-slab-v7-bold.woff → docs/css/fonts/Roboto-Slab-Bold.woff
diff --git a/...onts/RobotoSlab/roboto-slab-v7-bold.woff2 → docs/css/fonts/Roboto-Slab-Bold.woff2 b/...onts/RobotoSlab/roboto-slab-v7-bold.woff2 → docs/css/fonts/Roboto-Slab-Bold.woff2
diff --git a/...ts/RobotoSlab/roboto-slab-v7-regular.woff → docs/css/fonts/Roboto-Slab-Regular.woff b/...ts/RobotoSlab/roboto-slab-v7-regular.woff → docs/css/fonts/Roboto-Slab-Regular.woff
diff --git a/...s/RobotoSlab/roboto-slab-v7-regular.woff2 → docs/css/fonts/Roboto-Slab-Regular.woff2 b/...s/RobotoSlab/roboto-slab-v7-regular.woff2 → docs/css/fonts/Roboto-Slab-Regular.woff2
diff --git a/docs/fonts/fontawesome-webfont.eot → docs/css/fonts/fontawesome-webfont.eot b/docs/fonts/fontawesome-webfont.eot → docs/css/fonts/fontawesome-webfont.eot
diff --git a/docs/fonts/fontawesome-webfont.svg → docs/css/fonts/fontawesome-webfont.svg b/docs/fonts/fontawesome-webfont.svg → docs/css/fonts/fontawesome-webfont.svg
diff --git a/docs/fonts/fontawesome-webfont.ttf → docs/css/fonts/fontawesome-webfont.ttf b/docs/fonts/fontawesome-webfont.ttf → docs/css/fonts/fontawesome-webfont.ttf
diff --git a/docs/fonts/fontawesome-webfont.woff → docs/css/fonts/fontawesome-webfont.woff b/docs/fonts/fontawesome-webfont.woff → docs/css/fonts/fontawesome-webfont.woff
diff --git a/docs/fonts/fontawesome-webfont.woff2 → docs/css/fonts/fontawesome-webfont.woff2 b/docs/fonts/fontawesome-webfont.woff2 → docs/css/fonts/fontawesome-webfont.woff2
diff --git a/docs/fonts/Lato/lato-bolditalic.woff → docs/css/fonts/lato-bold-italic.woff b/docs/fonts/Lato/lato-bolditalic.woff → docs/css/fonts/lato-bold-italic.woff
diff --git a/docs/fonts/Lato/lato-bolditalic.woff2 → docs/css/fonts/lato-bold-italic.woff2 b/docs/fonts/Lato/lato-bolditalic.woff2 → docs/css/fonts/lato-bold-italic.woff2
diff --git a/docs/fonts/Lato/lato-bold.woff → docs/css/fonts/lato-bold.woff b/docs/fonts/Lato/lato-bold.woff → docs/css/fonts/lato-bold.woff
diff --git a/docs/fonts/Lato/lato-bold.woff2 → docs/css/fonts/lato-bold.woff2 b/docs/fonts/Lato/lato-bold.woff2 → docs/css/fonts/lato-bold.woff2
diff --git a/docs/fonts/Lato/lato-italic.woff → docs/css/fonts/lato-normal-italic.woff b/docs/fonts/Lato/lato-italic.woff → docs/css/fonts/lato-normal-italic.woff
diff --git a/docs/fonts/Lato/lato-italic.woff2 → docs/css/fonts/lato-normal-italic.woff2 b/docs/fonts/Lato/lato-italic.woff2 → docs/css/fonts/lato-normal-italic.woff2
diff --git a/docs/fonts/Lato/lato-regular.woff → docs/css/fonts/lato-normal.woff b/docs/fonts/Lato/lato-regular.woff → docs/css/fonts/lato-normal.woff
diff --git a/docs/fonts/Lato/lato-regular.woff2 → docs/css/fonts/lato-normal.woff2 b/docs/fonts/Lato/lato-regular.woff2 → docs/css/fonts/lato-normal.woff2
diff --git a/docs/css/theme.css b/docs/css/theme.css
diff --git a/docs/css/theme_extra.css b/docs/css/theme_extra.css
@@ -122,7 +122,7 @@ form .search-query {
 
 /*
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- * Override borders to avoid wierdness on narrow tables.
+ * Override borders to avoid weirdness on narrow tables.
  *
  * https://github.com/mkdocs/mkdocs/issues/834
  * https://github.com/mkdocs/mkdocs/pull/1034

diff --git a/docs/downstream/index.html b/docs/downstream/index.html
@@ -1,65 +1,59 @@
 <!DOCTYPE html>
-<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
-<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<html class="writer-html5" lang="en" >
 <head>
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-
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-  <link rel="canonical" href="https://mrcieu.github.io/gwas2vcf/downstream/">
-  <link rel="shortcut icon" href="../img/favicon.ico">
-  <title>Downstream analyses - gwas2vcf</title>
-  <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Lato:400,700|Roboto+Slab:400,700|Inconsolata:400,700" />
-
-  <link rel="stylesheet" href="../css/theme.css" />
-  <link rel="stylesheet" href="../css/theme_extra.css" />
-  <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/10.5.0/styles/github.min.css" />
-
-  <script>
-    // Current page data
-    var mkdocs_page_name = "Downstream analyses";
-    var mkdocs_page_input_path = "downstream.md";
-    var mkdocs_page_url = "/gwas2vcf/downstream/";
-  </script>
-
-  <script src="../js/jquery-2.1.1.min.js" defer></script>
-  <script src="../js/modernizr-2.8.3.min.js" defer></script>
-  <script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/10.5.0/highlight.min.js"></script>
-  <script>hljs.initHighlightingOnLoad();</script> 
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><link rel="canonical" href="https://mrcieu.github.io/gwas2vcf/downstream/" />
+      <link rel="shortcut icon" href="../img/favicon.ico" />
+    <title>Downstream analyses - gwas2vcf</title>
+    <link rel="stylesheet" href="../css/theme.css" />
+    <link rel="stylesheet" href="../css/theme_extra.css" />
+        <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/10.5.0/styles/github.min.css" />
+
+      <script>
+        // Current page data
+        var mkdocs_page_name = "Downstream analyses";
+        var mkdocs_page_input_path = "downstream.md";
+        var mkdocs_page_url = "/gwas2vcf/downstream/";
+      </script>
+
+    <script src="../js/jquery-3.6.0.min.js" defer></script>
+    <!--[if lt IE 9]>
+      <script src="../js/html5shiv.min.js"></script>
+    <![endif]-->
+      <script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/10.5.0/highlight.min.js"></script>
+      <script>hljs.initHighlightingOnLoad();</script> 
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+          <a href=".." class="icon icon-home"> gwas2vcf
+        </a><div role="search">
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-                    </li>
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-                <ul class="current">
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+      <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
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+                <li class="toctree-l1"><a class="reference internal" href="../install/">Install</a>
+                </li>
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+              <ul>
+                <li class="toctree-l1"><a class="reference internal" href="../tutorial/">Tutorial</a>
+                </li>
+              </ul>
+              <ul class="current">
+                <li class="toctree-l1 current"><a class="reference internal current" href="./">Downstream analyses</a>
     <ul class="current">
     <li class="toctree-l2"><a class="reference internal" href="#data">Data</a>
     </li>
@@ -114,40 +108,30 @@
         </ul>
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+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+            <div class="section" itemprop="articleBody">
 
                 <h1 id="working-with-gwas-vcf">Working with GWAS-VCF</h1>
 <p>See below examples of working with GWAS-VCF. Let us know if you have other use cases through the <a href="https://github.com/MRCIEU/gwas2vcf/issues">issues</a> page!</p>
@@ -306,35 +290,28 @@ <h4 id="check-the-file-format-is-valid">Check the file format is valid</h4>
 </code></pre>
 
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diff --git a/docs/fonts/Lato/lato-bold.eot b/docs/fonts/Lato/lato-bold.eot
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