Merge pull request #99 from AndreaGuarracino/patch-2

several fixes in the website, added links to video talk and poster, new pangenome generation workflow

4 files changed, 6 insertions, 56 deletions

diff --git a/doc/blog/using-covid-19-pubseq-part2.html b/doc/blog/using-covid-19-pubseq-part2.html
index c047441..c041ebe 100644
--- a/doc/blog/using-covid-19-pubseq-part2.html
+++ b/doc/blog/using-covid-19-pubseq-part2.html
@@ -259,39 +259,12 @@ for the JavaScript code in this tag.
 </ul>
 </div>
 </div>
-<p>
-As part of the COVID-19 Biohackathon 2020 we formed a working group to
-create a COVID-19 Public Sequence Resource (COVID-19 PubSeq) for
-Corona virus sequences. The general idea is to create a repository
-that has a low barrier to entry for uploading sequence data using best
-practices. I.e., data published with a creative commons 4.0 (CC-4.0)
-license with metadata using state-of-the art standards and, perhaps
-most importantly, providing standardised workflows that get triggered
-on upload, so that results are immediately available in standardised
-data formats.
-</p>
 
 <div id="outline-container-org7942167" class="outline-2">
 <h2 id="org7942167"><span class="section-number-2">1</span> Finding output of workflows</h2>
 <div class="outline-text-2" id="text-1">
-<p>
-As part of the COVID-19 Biohackathon 2020 we formed a working group to
-create a COVID-19 Public Sequence Resource (COVID-19 PubSeq) for
-Corona virus sequences. The general idea is to create a repository
-that has a low barrier to entry for uploading sequence data using best
-practices. I.e., data published with a creative commons 4.0 (CC-4.0)
-license with metadata using state-of-the art standards and, perhaps
-most importantly, providing standardised workflows that get triggered
-on upload, so that results are immediately available in standardised
-data formats.
-</p>
-</div>
-</div>
 
-<div id="outline-container-org0022bbe" class="outline-2">
-<h2 id="org0022bbe"><span class="section-number-2">2</span> Introduction</h2>
-<div class="outline-text-2" id="text-2">
-<p>
+ <p>
 We are using Arvados to run common workflow language (CWL) pipelines.
 The most recent output is on display on a <a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca">web page</a> (with time stamp)
 and a full list is generated <a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/">here</a>. It is nice to start up, but for
@@ -302,7 +275,7 @@ want to wade through thousands of output files!
 </div>
 
 <div id="outline-container-org3929710" class="outline-2">
-<h2 id="org3929710"><span class="section-number-2">3</span> The Arvados file interface</h2>
+<h2 id="org3929710"><span class="section-number-2">2</span> The Arvados file interface</h2>
 <div class="outline-text-2" id="text-3">
 <p>
 Arvados has the web server, but it also has a REST API and associated
@@ -384,7 +357,7 @@ arv-get 2be6af7b4741f2a5c5f8ff2bc6152d73+1955623+Ab9ad65d7fe958a053b3a57d545839d
 </div>
 
 <div id="outline-container-orgc4dba6e" class="outline-2">
-<h2 id="orgc4dba6e"><span class="section-number-2">4</span> Using the Arvados API</h2>
+<h2 id="orgc4dba6e"><span class="section-number-2">3</span> TODO Using the Arvados API</h2>
 </div>
 </div>
 <div id="postamble" class="status">
diff --git a/doc/blog/using-covid-19-pubseq-part2.org b/doc/blog/using-covid-19-pubseq-part2.org
index d2a1cbc..349fd06 100644
--- a/doc/blog/using-covid-19-pubseq-part2.org
+++ b/doc/blog/using-covid-19-pubseq-part2.org
@@ -8,36 +8,13 @@
 #+HTML_LINK_HOME: http://covid19.genenetwork.org
 #+HTML_HEAD: <link rel="Blog stylesheet" type="text/css" href="blog.css" />
 
-As part of the COVID-19 Biohackathon 2020 we formed a working group to
-create a COVID-19 Public Sequence Resource (COVID-19 PubSeq) for
-Corona virus sequences. The general idea is to create a repository
-that has a low barrier to entry for uploading sequence data using best
-practices. I.e., data published with a creative commons 4.0 (CC-4.0)
-license with metadata using state-of-the art standards and, perhaps
-most importantly, providing standardised workflows that get triggered
-on upload, so that results are immediately available in standardised
-data formats.
-
 * Table of Contents                                                     :TOC:noexport:
  - [[#finding-output-of-workflows][Finding output of workflows]]
- - [[#introduction][Introduction]]
  - [[#the-arvados-file-interface][The Arvados file interface]]
  - [[#using-the-arvados-api][Using the Arvados API]]
 
 * Finding output of workflows
 
-As part of the COVID-19 Biohackathon 2020 we formed a working group to
-create a COVID-19 Public Sequence Resource (COVID-19 PubSeq) for
-Corona virus sequences. The general idea is to create a repository
-that has a low barrier to entry for uploading sequence data using best
-practices. I.e., data published with a creative commons 4.0 (CC-4.0)
-license with metadata using state-of-the art standards and, perhaps
-most importantly, providing standardised workflows that get triggered
-on upload, so that results are immediately available in standardised
-data formats.
-
-* Introduction
-
 We are using Arvados to run common workflow language (CWL) pipelines.
 The most recent output is on display on a [[https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca][web page]] (with time stamp)
 and a full list is generated [[https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/][here]]. It is nice to start up, but for
@@ -81,4 +58,4 @@ its listed UUID:
 
 : arv-get 2be6af7b4741f2a5c5f8ff2bc6152d73+1955623+Ab9ad65d7fe958a053b3a57d545839de18290843a@5ed7f3c5
 
-* Using the Arvados API
+* TODO Using the Arvados API
diff --git a/doc/blog/using-covid-19-pubseq-part3.html b/doc/blog/using-covid-19-pubseq-part3.html
index 91879b0..df4a286 100644
--- a/doc/blog/using-covid-19-pubseq-part3.html
+++ b/doc/blog/using-covid-19-pubseq-part3.html
@@ -625,7 +625,7 @@ The web interface using this exact same script so it should just work
 <h3 id="org39adf09"><span class="section-number-3">6.2</span> Example: uploading bulk GenBank sequences</h3>
 <div class="outline-text-3" id="text-6-2">
 <p>
-We also use above script to bulk upload GenBank sequences with a <a href="https://github.com/arvados/bh20-seq-resource/blob/master/scripts/from_genbank_to_fasta_and_yaml.py">FASTA
+We also use above script to bulk upload GenBank sequences with a <a href="https://github.com/arvados/bh20-seq-resource/blob/master/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py">FASTA
 and YAML</a> extractor specific for GenBank. This means that the steps we
 took above for uploading a GenBank sequence are already automated.
 </p>
diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org
index 03f37ab..e8fee36 100644
--- a/doc/blog/using-covid-19-pubseq-part3.org
+++ b/doc/blog/using-covid-19-pubseq-part3.org
@@ -234,6 +234,6 @@ The web interface using this exact same script so it should just work
 
 ** Example: uploading bulk GenBank sequences
 
-We also use above script to bulk upload GenBank sequences with a [[https://github.com/arvados/bh20-seq-resource/blob/master/scripts/from_genbank_to_fasta_and_yaml.py][FASTA
+We also use above script to bulk upload GenBank sequences with a [[https://github.com/arvados/bh20-seq-resource/blob/master/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py][FASTA
 and YAML]] extractor specific for GenBank. This means that the steps we
 took above for uploading a GenBank sequence are already automated.