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| author | AndreaGuarracino | 2020-07-26 18:02:41 +0200 |
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| committer | AndreaGuarracino | 2020-07-27 12:14:24 +0200 |
| commit | 8e052cb7355eed7ce4d7075b23c9b0439285f84e (patch) | |
| tree | da4bec31ef119f6f67a912f53235dfe26a1ef1f6 /doc/blog/using-covid-19-pubseq-part2.html | |
| parent | 0bd9dadb8a2dabcd06deb9df3b1082f7e1d993fe (diff) | |
| download | bh20-seq-resource-8e052cb7355eed7ce4d7075b23c9b0439285f84e.tar.gz bh20-seq-resource-8e052cb7355eed7ce4d7075b23c9b0439285f84e.tar.lz bh20-seq-resource-8e052cb7355eed7ce4d7075b23c9b0439285f84e.zip | |
updated org files, removing unuseful information and adding the BCC2020 video talk and poster links in the about page
Diffstat (limited to 'doc/blog/using-covid-19-pubseq-part2.html')
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part2.html | 33 |
1 files changed, 3 insertions, 30 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"> |