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authorPeter Amstutz2020-08-05 16:06:11 -0400
committerGitHub2020-08-05 16:06:11 -0400
commitfdb1b012fc04ee07f401541e181e28fe442c9454 (patch)
tree8486db1087692dffcea9d93814e436d9cf150b47 /doc/blog
parent86f31ef60f65a820bf9ac25c3fc01c88f2a9ebfe (diff)
parent2d20bf90497588a297ca98a78ee0fbbcadf95569 (diff)
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Merge pull request #99 from AndreaGuarracino/patch-2
several fixes in the website, added links to video talk and poster, new pangenome generation workflow
Diffstat (limited to 'doc/blog')
-rw-r--r--doc/blog/using-covid-19-pubseq-part2.html33
-rw-r--r--doc/blog/using-covid-19-pubseq-part2.org25
-rw-r--r--doc/blog/using-covid-19-pubseq-part3.html2
-rw-r--r--doc/blog/using-covid-19-pubseq-part3.org2
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.