From 5f36706b7c9dc1786e47848f0ce8aabd4e7ab851 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 30 May 2020 10:46:28 -0500
Subject: BLOG: checkout output

---
 doc/web/download.html | 99 ++++++++++++++++++++++++++-------------------------
 doc/web/download.org  |  5 ++-
 2 files changed, 55 insertions(+), 49 deletions(-)

(limited to 'doc/web')
diff --git a/doc/web/download.html b/doc/web/download.html
index 2fde013..001b071 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>
-<!-- 2020-05-29 Fri 08:27 -->
+<!-- 2020-05-30 Sat 10:40 -->
 <meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
 <meta name="viewport" content="width=device-width, initial-scale=1" />
 <title>Download</title>
@@ -247,42 +247,45 @@ for the JavaScript code in this tag.
 <h2>Table of Contents</h2>
 <div id="text-table-of-contents">
 <ul>
-<li><a href="#orgdde8653">1. Workflow runs</a></li>
-<li><a href="#org406920c">2. FASTA files</a></li>
-<li><a href="#org8e639a6">3. Metadata</a></li>
-<li><a href="#org940e0a9">4. Pangenome</a>
+<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>
 <ul>
-<li><a href="#org032f85b">4.1. Pangenome GFA format</a></li>
-<li><a href="#org0c3f155">4.2. Pangenome in ODGI format</a></li>
-<li><a href="#org08a5353">4.3. Pangenome RDF format</a></li>
-<li><a href="#org369f04f">4.4. Pangenome Browser format</a></li>
+<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>
 </ul>
 </li>
-<li><a href="#orge6e1f1b">5. Log of workflow output</a></li>
-<li><a href="#org90d906c">6. All files</a></li>
-<li><a href="#org95b1d68">7. Planned</a>
+<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>
 <ul>
-<li><a href="#org629d3ef">7.1. Raw sequence data</a></li>
-<li><a href="#org2f745c7">7.2. Multiple Sequence Alignment (MSA)</a></li>
-<li><a href="#org8d3edf7">7.3. Phylogenetic tree</a></li>
-<li><a href="#orge0c103c">7.4. Protein prediction</a></li>
+<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>
 </ul>
 </li>
 </ul>
 </div>
 </div>
 
-<div id="outline-container-orgdde8653" class="outline-2">
-<h2 id="orgdde8653"><span class="section-number-2">1</span> Workflow runs</h2>
+<div id="outline-container-orgcde4e6b" class="outline-2">
+<h2 id="orgcde4e6b"><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/container_requests/lugli-xvhdp-bhhk4nxx1lch5od">here</a>.
+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
+the workflows that ran under <code>Processes</code>. Output (also intermediate)
+is listed under <code>Data collections</code>. All current data is listed
+<a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/">here</a>. Note that it takes time for a run to complete and show.
 </p>
 </div>
 </div>
 
-<div id="outline-container-org406920c" class="outline-2">
-<h2 id="org406920c"><span class="section-number-2">2</span> FASTA files</h2>
+<div id="outline-container-org1b46d7e" class="outline-2">
+<h2 id="org1b46d7e"><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
@@ -292,8 +295,8 @@ also provide a single file <a href="https://collections.lugli.arvadosapi.com/c=l
 </div>
 </div>
 
-<div id="outline-container-org8e639a6" class="outline-2">
-<h2 id="org8e639a6"><span class="section-number-2">3</span> Metadata</h2>
+<div id="outline-container-orgf2db570" class="outline-2">
+<h2 id="orgf2db570"><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
@@ -315,8 +318,8 @@ graph can be downloaded from below Pangenome RDF format.
 </div>
 </div>
 
-<div id="outline-container-org940e0a9" class="outline-2">
-<h2 id="org940e0a9"><span class="section-number-2">4</span> Pangenome</h2>
+<div id="outline-container-org9f89b24" class="outline-2">
+<h2 id="org9f89b24"><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
@@ -324,8 +327,8 @@ Pangenome data is made available in multiple guises. Variation graphs
 </p>
 </div>
 
-<div id="outline-container-org032f85b" class="outline-3">
-<h3 id="org032f85b"><span class="section-number-3">4.1</span> Pangenome GFA format</h3>
+<div id="outline-container-org436ee36" class="outline-3">
+<h3 id="org436ee36"><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
@@ -334,8 +337,8 @@ by tools such as <a href="https://github.com/vgteam/vg">vgtools</a>.
 </div>
 </div>
 
-<div id="outline-container-org0c3f155" class="outline-3">
-<h3 id="org0c3f155"><span class="section-number-3">4.2</span> Pangenome in ODGI format</h3>
+<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 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
@@ -344,8 +347,8 @@ implementation.
 </div>
 </div>
 
-<div id="outline-container-org08a5353" class="outline-3">
-<h3 id="org08a5353"><span class="section-number-3">4.3</span> Pangenome RDF format</h3>
+<div id="outline-container-org220b6cb" class="outline-3">
+<h3 id="org220b6cb"><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
@@ -356,8 +359,8 @@ graph can be downloaded from
 </div>
 
 
-<div id="outline-container-org369f04f" class="outline-3">
-<h3 id="org369f04f"><span class="section-number-3">4.4</span> Pangenome Browser format</h3>
+<div id="outline-container-org78f267a" class="outline-3">
+<h3 id="org78f267a"><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
@@ -368,8 +371,8 @@ Pangenome browser.
 </div>
 </div>
 
-<div id="outline-container-orge6e1f1b" class="outline-2">
-<h2 id="orge6e1f1b"><span class="section-number-2">5</span> Log of workflow output</h2>
+<div id="outline-container-org8cced34" class="outline-2">
+<h2 id="org8cced34"><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.
@@ -377,8 +380,8 @@ Including in below link is a log file of the last workflow runs.
 </div>
 </div>
 
-<div id="outline-container-org90d906c" class="outline-2">
-<h2 id="org90d906c"><span class="section-number-2">6</span> All files</h2>
+<div id="outline-container-org9d23c51" class="outline-2">
+<h2 id="org9d23c51"><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>
@@ -386,16 +389,16 @@ Including in below link is a log file of the last workflow runs.
 </div>
 </div>
 
-<div id="outline-container-org95b1d68" class="outline-2">
-<h2 id="org95b1d68"><span class="section-number-2">7</span> Planned</h2>
+<div id="outline-container-org105d2d4" class="outline-2">
+<h2 id="org105d2d4"><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-org629d3ef" class="outline-3">
-<h3 id="org629d3ef"><span class="section-number-3">7.1</span> Raw sequence data</h3>
+<div id="outline-container-org52bb570" class="outline-3">
+<h3 id="org52bb570"><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>.
@@ -403,8 +406,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/16">fastq track
 </div>
 </div>
 
-<div id="outline-container-org2f745c7" class="outline-3">
-<h3 id="org2f745c7"><span class="section-number-3">7.2</span> Multiple Sequence Alignment (MSA)</h3>
+<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 class="outline-text-3" id="text-7-2">
 <p>
 See <a href="https://github.com/arvados/bh20-seq-resource/issues/11">MSA tracker</a>.
@@ -412,8 +415,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/11">MSA tracker
 </div>
 </div>
 
-<div id="outline-container-org8d3edf7" class="outline-3">
-<h3 id="org8d3edf7"><span class="section-number-3">7.3</span> Phylogenetic tree</h3>
+<div id="outline-container-org9ccf15c" class="outline-3">
+<h3 id="org9ccf15c"><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>.
@@ -421,8 +424,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/43">Phylo track
 </div>
 </div>
 
-<div id="outline-container-orge0c103c" class="outline-3">
-<h3 id="orge0c103c"><span class="section-number-3">7.4</span> Protein prediction</h3>
+<div id="outline-container-org31c2b68" class="outline-3">
+<h3 id="org31c2b68"><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.
@@ -432,7 +435,7 @@ We aim to make protein predictions available.
 </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 2020-05-29 Fri 08:27</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 2020-05-30 Sat 10:40</small>.
 </div>
 </body>
 </html>
diff --git a/doc/web/download.org b/doc/web/download.org
index 2781d67..da6a9a7 100644
--- a/doc/web/download.org
+++ b/doc/web/download.org
@@ -20,7 +20,10 @@
 
 * Workflow runs
 
-The last runs can be viewed [[https://workbench.lugli.arvadosapi.com/container_requests/lugli-xvhdp-bhhk4nxx1lch5od][here]].
+The last runs can be viewed [[https://workbench.lugli.arvadosapi.com/projects/lugli-j7d0g-y4k4uswcqi3ku56#Subprojects][here]]. If you click on a run you can see
+the workflows that ran under ~Processes~. Output (also intermediate)
+is listed under ~Data collections~. All current data is listed
+[[https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/][here]]. Note that it takes time for a run to complete and show.
 
 * FASTA files
 
-- 
cgit v1.2.3

