From 9fb2d889105753b52ba6380f7f1e6f8732daefe2 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 12 Jun 2020 04:58:15 -0500
Subject: Added github repo to Download

---
 doc/web/download.html | 106 ++++++++++++++++++++++++++++----------------------
 1 file changed, 59 insertions(+), 47 deletions(-)

(limited to 'doc/web/download.html')
diff --git a/doc/web/download.html b/doc/web/download.html
index 001b071..1d196a0 100644
--- a/doc/web/download.html
+++ b/doc/web/download.html
@@ -3,7 +3,7 @@
 "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
 <head>
-<!-- 2020-05-30 Sat 10:40 -->
+<!-- 2020-06-12 Fri 04:41 -->
 <meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
 <meta name="viewport" content="width=device-width, initial-scale=1" />
 <title>Download</title>
@@ -247,33 +247,34 @@ for the JavaScript code in this tag.
 <h2>Table of Contents</h2>
 <div id="text-table-of-contents">
 <ul>
-<li><a href="#orgcde4e6b">1. Workflow runs</a></li>
-<li><a href="#org1b46d7e">2. FASTA files</a></li>
-<li><a href="#orgf2db570">3. Metadata</a></li>
-<li><a href="#org9f89b24">4. Pangenome</a>
+<li><a href="#orgcd3d82f">1. Workflow runs</a></li>
+<li><a href="#org9aff936">2. FASTA files</a></li>
+<li><a href="#orgc3e953c">3. Metadata</a></li>
+<li><a href="#orgc9c55c4">4. Pangenome</a>
 <ul>
-<li><a href="#org436ee36">4.1. Pangenome GFA format</a></li>
-<li><a href="#org6cd667b">4.2. Pangenome in ODGI format</a></li>
-<li><a href="#org220b6cb">4.3. Pangenome RDF format</a></li>
-<li><a href="#org78f267a">4.4. Pangenome Browser format</a></li>
+<li><a href="#org82c3ce9">4.1. Pangenome GFA format</a></li>
+<li><a href="#orgf63e9f7">4.2. Pangenome in ODGI format</a></li>
+<li><a href="#org8faf32f">4.3. Pangenome RDF format</a></li>
+<li><a href="#org0c452f6">4.4. Pangenome Browser format</a></li>
 </ul>
 </li>
-<li><a href="#org8cced34">5. Log of workflow output</a></li>
-<li><a href="#org9d23c51">6. All files</a></li>
-<li><a href="#org105d2d4">7. Planned</a>
+<li><a href="#org4707094">5. Log of workflow output</a></li>
+<li><a href="#orgd4d8f91">6. All files</a></li>
+<li><a href="#org237b3cf">7. Planned</a>
 <ul>
-<li><a href="#org52bb570">7.1. Raw sequence data</a></li>
-<li><a href="#org68c178c">7.2. Multiple Sequence Alignment (MSA)</a></li>
-<li><a href="#org9ccf15c">7.3. Phylogenetic tree</a></li>
-<li><a href="#org31c2b68">7.4. Protein prediction</a></li>
+<li><a href="#org66e03ac">7.1. Raw sequence data</a></li>
+<li><a href="#orgdfae1b9">7.2. Multiple Sequence Alignment (MSA)</a></li>
+<li><a href="#orgaedc43e">7.3. Phylogenetic tree</a></li>
+<li><a href="#org19a6a11">7.4. Protein prediction</a></li>
 </ul>
 </li>
+<li><a href="#org49778b7">8. Source code</a></li>
 </ul>
 </div>
 </div>
 
-<div id="outline-container-orgcde4e6b" class="outline-2">
-<h2 id="orgcde4e6b"><span class="section-number-2">1</span> Workflow runs</h2>
+<div id="outline-container-orgcd3d82f" class="outline-2">
+<h2 id="orgcd3d82f"><span class="section-number-2">1</span> Workflow runs</h2>
 <div class="outline-text-2" id="text-1">
 <p>
 The last runs can be viewed <a href="https://workbench.lugli.arvadosapi.com/projects/lugli-j7d0g-y4k4uswcqi3ku56#Subprojects">here</a>. If you click on a run you can see
@@ -284,8 +285,8 @@ is listed under <code>Data collections</code>. All current data is listed
 </div>
 </div>
 
-<div id="outline-container-org1b46d7e" class="outline-2">
-<h2 id="org1b46d7e"><span class="section-number-2">2</span> FASTA files</h2>
+<div id="outline-container-org9aff936" class="outline-2">
+<h2 id="org9aff936"><span class="section-number-2">2</span> FASTA files</h2>
 <div class="outline-text-2" id="text-2">
 <p>
 The <b>public sequence resource</b> provides all uploaded sequences as
@@ -295,8 +296,8 @@ also provide a single file <a href="https://collections.lugli.arvadosapi.com/c=l
 </div>
 </div>
 
-<div id="outline-container-orgf2db570" class="outline-2">
-<h2 id="orgf2db570"><span class="section-number-2">3</span> Metadata</h2>
+<div id="outline-container-orgc3e953c" class="outline-2">
+<h2 id="orgc3e953c"><span class="section-number-2">3</span> Metadata</h2>
 <div class="outline-text-2" id="text-3">
 <p>
 Metadata can be downloaded as <a href="https://www.w3.org/TR/turtle/">Turtle RDF</a> as a <a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/mergedmetadata.ttl">mergedmetadat.ttl</a> which
@@ -318,8 +319,8 @@ graph can be downloaded from below Pangenome RDF format.
 </div>
 </div>
 
-<div id="outline-container-org9f89b24" class="outline-2">
-<h2 id="org9f89b24"><span class="section-number-2">4</span> Pangenome</h2>
+<div id="outline-container-orgc9c55c4" class="outline-2">
+<h2 id="orgc9c55c4"><span class="section-number-2">4</span> Pangenome</h2>
 <div class="outline-text-2" id="text-4">
 <p>
 Pangenome data is made available in multiple guises. Variation graphs
@@ -327,8 +328,8 @@ Pangenome data is made available in multiple guises. Variation graphs
 </p>
 </div>
 
-<div id="outline-container-org436ee36" class="outline-3">
-<h3 id="org436ee36"><span class="section-number-3">4.1</span> Pangenome GFA format</h3>
+<div id="outline-container-org82c3ce9" class="outline-3">
+<h3 id="org82c3ce9"><span class="section-number-3">4.1</span> Pangenome GFA format</h3>
 <div class="outline-text-3" id="text-4-1">
 <p>
 <a href="https://github.com/GFA-spec/GFA-spec">GFA</a> is a standard for graphical fragment assembly and consumed
@@ -337,8 +338,8 @@ by tools such as <a href="https://github.com/vgteam/vg">vgtools</a>.
 </div>
 </div>
 
-<div id="outline-container-org6cd667b" class="outline-3">
-<h3 id="org6cd667b"><span class="section-number-3">4.2</span> Pangenome in ODGI format</h3>
+<div id="outline-container-orgf63e9f7" class="outline-3">
+<h3 id="orgf63e9f7"><span class="section-number-3">4.2</span> Pangenome in ODGI format</h3>
 <div class="outline-text-3" id="text-4-2">
 <p>
 <a href="https://github.com/vgteam/odgi">ODGI</a> is a format that supports an optimised dynamic genome/graph
@@ -347,8 +348,8 @@ implementation.
 </div>
 </div>
 
-<div id="outline-container-org220b6cb" class="outline-3">
-<h3 id="org220b6cb"><span class="section-number-3">4.3</span> Pangenome RDF format</h3>
+<div id="outline-container-org8faf32f" class="outline-3">
+<h3 id="org8faf32f"><span class="section-number-3">4.3</span> Pangenome RDF format</h3>
 <div class="outline-text-3" id="text-4-3">
 <p>
 An RDF file that includes the sequences themselves in a variation
@@ -359,8 +360,8 @@ graph can be downloaded from
 </div>
 
 
-<div id="outline-container-org78f267a" class="outline-3">
-<h3 id="org78f267a"><span class="section-number-3">4.4</span> Pangenome Browser format</h3>
+<div id="outline-container-org0c452f6" class="outline-3">
+<h3 id="org0c452f6"><span class="section-number-3">4.4</span> Pangenome Browser format</h3>
 <div class="outline-text-3" id="text-4-4">
 <p>
 The many JSON files that are named as
@@ -371,8 +372,8 @@ Pangenome browser.
 </div>
 </div>
 
-<div id="outline-container-org8cced34" class="outline-2">
-<h2 id="org8cced34"><span class="section-number-2">5</span> Log of workflow output</h2>
+<div id="outline-container-org4707094" class="outline-2">
+<h2 id="org4707094"><span class="section-number-2">5</span> Log of workflow output</h2>
 <div class="outline-text-2" id="text-5">
 <p>
 Including in below link is a log file of the last workflow runs.
@@ -380,8 +381,8 @@ Including in below link is a log file of the last workflow runs.
 </div>
 </div>
 
-<div id="outline-container-org9d23c51" class="outline-2">
-<h2 id="org9d23c51"><span class="section-number-2">6</span> All files</h2>
+<div id="outline-container-orgd4d8f91" class="outline-2">
+<h2 id="orgd4d8f91"><span class="section-number-2">6</span> All files</h2>
 <div class="outline-text-2" id="text-6">
 <p>
 <a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/">https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/</a>
@@ -389,16 +390,16 @@ Including in below link is a log file of the last workflow runs.
 </div>
 </div>
 
-<div id="outline-container-org105d2d4" class="outline-2">
-<h2 id="org105d2d4"><span class="section-number-2">7</span> Planned</h2>
+<div id="outline-container-org237b3cf" class="outline-2">
+<h2 id="org237b3cf"><span class="section-number-2">7</span> Planned</h2>
 <div class="outline-text-2" id="text-7">
 <p>
 We are planning the add the following output (see also
 </p>
 </div>
 
-<div id="outline-container-org52bb570" class="outline-3">
-<h3 id="org52bb570"><span class="section-number-3">7.1</span> Raw sequence data</h3>
+<div id="outline-container-org66e03ac" class="outline-3">
+<h3 id="org66e03ac"><span class="section-number-3">7.1</span> Raw sequence data</h3>
 <div class="outline-text-3" id="text-7-1">
 <p>
 See <a href="https://github.com/arvados/bh20-seq-resource/issues/16">fastq tracker</a> and <a href="https://github.com/arvados/bh20-seq-resource/issues/63">BAM tracker</a>.
@@ -406,8 +407,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/16">fastq track
 </div>
 </div>
 
-<div id="outline-container-org68c178c" class="outline-3">
-<h3 id="org68c178c"><span class="section-number-3">7.2</span> Multiple Sequence Alignment (MSA)</h3>
+<div id="outline-container-orgdfae1b9" class="outline-3">
+<h3 id="orgdfae1b9"><span class="section-number-3">7.2</span> Multiple Sequence Alignment (MSA)</h3>
 <div class="outline-text-3" id="text-7-2">
 <p>
 See <a href="https://github.com/arvados/bh20-seq-resource/issues/11">MSA tracker</a>.
@@ -415,8 +416,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/11">MSA tracker
 </div>
 </div>
 
-<div id="outline-container-org9ccf15c" class="outline-3">
-<h3 id="org9ccf15c"><span class="section-number-3">7.3</span> Phylogenetic tree</h3>
+<div id="outline-container-orgaedc43e" class="outline-3">
+<h3 id="orgaedc43e"><span class="section-number-3">7.3</span> Phylogenetic tree</h3>
 <div class="outline-text-3" id="text-7-3">
 <p>
 See <a href="https://github.com/arvados/bh20-seq-resource/issues/43">Phylo tracker</a>.
@@ -424,8 +425,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/43">Phylo track
 </div>
 </div>
 
-<div id="outline-container-org31c2b68" class="outline-3">
-<h3 id="org31c2b68"><span class="section-number-3">7.4</span> Protein prediction</h3>
+<div id="outline-container-org19a6a11" class="outline-3">
+<h3 id="org19a6a11"><span class="section-number-3">7.4</span> Protein prediction</h3>
 <div class="outline-text-3" id="text-7-4">
 <p>
 We aim to make protein predictions available.
@@ -433,9 +434,20 @@ We aim to make protein predictions available.
 </div>
 </div>
 </div>
+
+<div id="outline-container-org49778b7" class="outline-2">
+<h2 id="org49778b7"><span class="section-number-2">8</span> Source code</h2>
+<div class="outline-text-2" id="text-8">
+<p>
+All source code for this website and tooling is available
+from
+<a href="https://github.com/arvados/bh20-seq-resource">https://github.com/arvados/bh20-seq-resource</a>
+</p>
+</div>
+</div>
 </div>
 <div id="postamble" class="status">
-<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-05-30 Sat 10:40</small>.
+<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-06-12 Fri 04:41</small>.
 </div>
 </body>
 </html>
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