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<div id="org-div-home-and-up">
<a accesskey="h" href=""> UP </a>
|
<a accesskey="H" href="http://covid19.genenetwork.org"> HOME </a>
</div><div id="content">
<h1 class="title">COVID-19 PubSeq (part 2)</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org7942167">1. Finding output of workflows</a></li>
<li><a href="#org0022bbe">2. Introduction</a></li>
<li><a href="#org3929710">3. The Arvados file interface</a></li>
<li><a href="#orgc4dba6e">4. Using the Arvados API</a></li>
</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>
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
most users we need a dedicated and themed results page. People don't
want to wade through thousands of output files!
</p>
</div>
</div>
<div id="outline-container-org3929710" class="outline-2">
<h2 id="org3929710"><span class="section-number-2">3</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
command line tools. We are already using the <a href="https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/main.py#L27">API</a> to upload data. If
you follow the pip or <a href="../INSTALL.md">../INSTALL.md</a> GNU Guix instructions for
installing Arvados API you'll find the following command line tools
(also documented <a href="https://doc.arvados.org/v2.0/sdk/cli/subcommands.html">here</a>):
</p>
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
<col class="org-left" />
<col class="org-left" />
</colgroup>
<thead>
<tr>
<th scope="col" class="org-left">Command</th>
<th scope="col" class="org-left">Description</th>
</tr>
</thead>
<tbody>
<tr>
<td class="org-left">arv-ls</td>
<td class="org-left">list files in Arvados</td>
</tr>
<tr>
<td class="org-left">arv-put</td>
<td class="org-left">upload a file to Arvados</td>
</tr>
<tr>
<td class="org-left">arv-get</td>
<td class="org-left">get a textual representation of Arvados objects from the command line. The output can be limited to a subset of the object’s fields. This command can be used with only the knowledge of an object’s UUID</td>
</tr>
</tbody>
</table>
<p>
Now, this is a public instance so we can use the tokens from
the <a href="https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/main.py#L16">uploader</a>.
</p>
<div class="SOURCE">
<p>
export ARVADOS<sub>API</sub><sub>HOST</sub>='lugli.arvadosapi.com'
export ARVADOS<sub>API</sub><sub>TOKEN</sub>='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'
arv-ls lugli-4zz18-z513nlpqm03hpca
</p>
</div>
<p>
will list all files (the UUID we got from the Arvados results page). To
get the UUID of the files
</p>
<div class="SOURCE">
<p>
curl <a href="https://lugli.arvadosapi.com/arvados/v1/config">https://lugli.arvadosapi.com/arvados/v1/config</a> | jq .Users.AnonymousUserToken
env ARVADOS<sub>API</sub><sub>TOKEN</sub>=5o42qdxpxp5cj15jqjf7vnxx5xduhm4ret703suuoa3ivfglfh \
arv-get lugli-4zz18-z513nlpqm03hpca
</p>
</div>
<p>
and fetch one listed JSON file <code>chunk001_bin4000.schematic.json</code> with
its listed UUID:
</p>
<pre class="example">
arv-get 2be6af7b4741f2a5c5f8ff2bc6152d73+1955623+Ab9ad65d7fe958a053b3a57d545839de18290843a@5ed7f3c5
</pre>
</div>
</div>
<div id="outline-container-orgc4dba6e" class="outline-2">
<h2 id="orgc4dba6e"><span class="section-number-2">4</span> Using the Arvados API</h2>
</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 11:50</small>.
</div>
</body>
</html>
|
