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<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 - Arvados</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org10ef830">1. The Arvados Web Server</a></li>
<li><a href="#orgb6a7a42">2. The Arvados file interface</a></li>
<li><a href="#org0c7b94e">3. The PubSeq Arvados shell</a></li>
<li><a href="#org756005d">4. Wiring up CWL</a></li>
<li><a href="#orgf30b46f">5. Using the Arvados API</a></li>
<li><a href="#org3af3122">6. Troubleshooting</a></li>
</ul>
</div>
</div>
<div id="outline-container-org10ef830" class="outline-2">
<h2 id="org10ef830"><span class="section-number-2">1</span> The Arvados Web Server</h2>
<div class="outline-text-2" id="text-1">
<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 output list is generated <a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/">here</a>.
</p>
<p>
Arvados has a web front which allows navigation through input and output data,
workflows and the output of analysis pipelines (here CWL workflows).
</p>
<p>
<img src="static/image/arvados-workflow-output.png" />
</p>
</div>
</div>
<div id="outline-container-orgb6a7a42" class="outline-2">
<h2 id="orgb6a7a42"><span class="section-number-2">2</span> The Arvados file interface</h2>
<div class="outline-text-2" id="text-2">
<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="org-src-container">
<pre class="src src-sh"><span style="color: #ff8A65;">export</span> <span style="color: #ffcc80;">ARVADOS_API_HOST</span>=<span style="color: #9ccc65;">'lugli.arvadosapi.com'</span>
<span style="color: #ff8A65;">export</span> <span style="color: #ffcc80;">ARVADOS_API_TOKEN</span>=<span style="color: #9ccc65;">'2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'</span>
arv-ls lugli-4zz18-z513nlpqm03hpca
</pre>
</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="org-src-container">
<pre class="src src-sh">curl https://lugli.arvadosapi.com/arvados/v1/config | jq .Users.AnonymousUserToken
env <span style="color: #ffcc80;">ARVADOS_API_TOKEN</span>=5o42qdxpxp5cj15jqjf7vnxx5xduhm4ret703suuoa3ivfglfh <span style="color: #9ccc65;">\</span>
arv-get lugli-4zz18-z513nlpqm03hpca
</pre>
</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-org0c7b94e" class="outline-2">
<h2 id="org0c7b94e"><span class="section-number-2">3</span> The PubSeq Arvados shell</h2>
<div class="outline-text-2" id="text-3">
<p>
When you login to Arvados (you can request permission from us) it is
possible to upload an ssh key in your profile and get an shell prompt
with
</p>
<pre class="example">
ssh pjotrpbl@shell.lugli.arvadosapi.com
Linux ip-10-255-0-202 4.19.0-9-cloud-amd64 #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) x86_64
</pre>
<p>
It is a small Debian VM hosted on AWS somewhere. The PubSeq material
is mounted on <code>/data/pubseq</code>. The log is in <code>nohup.out</code>. Update/edit
the code (bh20-seq-resource git checkout) and restart the service (the
run script). The log says
</p>
<pre class="example">
you should have permission to read the log (nohup.out) update / edit the code (bh20-seq-resource git checkout) and restart the service (the run script)
</pre>
<p>
which means it will trigger the run on upload. The service is running as a
Python virtualenv:
</p>
<pre class="example">
/data/pubseq/bh20-seq-resource/venv3/bin/python3 /data/pubseq/bh20-seq-resource/venv3/bin/bh20-seq-analyzer --no-start-analysis
</pre>
<p>
and is restarted by a <code>run</code> script:
</p>
<pre class="example">
/data/pubseq/run [options]
</pre>
<p>
The run script kills the old process, sets up the API tokens, pulls
the git repo and starts a new run calling into
/data/pubseq/bh20-seq-resource/venv3/bin/bh20-seq-analyzer which is
essentially <a href="https://github.com/arvados/bh20-seq-resource/blob/2baa88b766ec540bd34b96599014dd16e393af39/bh20seqanalyzer/main.py#L354">monitoring</a> for uploads.
</p>
<p>
On <code>run --help</code>
</p>
<pre class="example" id="org93c3a8a">
optional arguments:
-h, --help show this help message and exit
--uploader-project UPLOADER_PROJECT
--pangenome-analysis-project PANGENOME_ANALYSIS_PROJECT
--fastq-project FASTQ_PROJECT
--validated-project VALIDATED_PROJECT
--workflow-def-project WORKFLOW_DEF_PROJECT
--pangenome-workflow-uuid PANGENOME_WORKFLOW_UUID
--fastq-workflow-uuid FASTQ_WORKFLOW_UUID
--exclude-list EXCLUDE_LIST
--latest-result-collection LATEST_RESULT_COLLECTION
--kickoff
--no-start-analysis
--once
--print-status PRINT_STATUS
--revalidate
</pre>
</div>
</div>
<div id="outline-container-org756005d" class="outline-2">
<h2 id="org756005d"><span class="section-number-2">4</span> Wiring up CWL</h2>
<div class="outline-text-2" id="text-4">
<p>
In above script <code>bh20-seq-analyzer</code> you can see that the <a href="https://www.commonwl.org/">Common
Workflow Language</a> (CWL) gets <a href="https://github.com/arvados/bh20-seq-resource/blob/2baa88b766ec540bd34b96599014dd16e393af39/bh20seqanalyzer/main.py#L233">triggered</a>; for example <a href="https://github.com/arvados/bh20-seq-resource/tree/master/workflows/fastq2fasta">fastq2fasta</a> which
is part of the main repo. The actual script is in <a href="https://github.com/arvados/bh20-seq-resource/blob/master/workflows/fastq2fasta/fastq2fasta.cwl">fastq2fasta.cwl</a> and
runs the following tools in sequence: bwa-mem, samtools-view,
samtools-sort, and bam2fasta.
</p>
<p>
It probably pays to familiarize yourself with CWL and its concepts. We
believe it has a lot going for it though CWL is some steps removed
from traditional shell scripts for running work flows. Main thing to
understand is that CWL is a separation of concerns, i.e.,
</p>
<ol class="org-ol">
<li>Data</li>
<li>Tools</li>
<li>Flow</li>
</ol>
<p>
and each of these are described separately. This contrasts largely
with shell scripts (though you can invoke shell scripts from CWL).
Also, CWL is written in JSON/YAML, which means everything can be parsed
as a tree and you can easily get visualisations such as
</p>
<p>
<a href="https://hpc.guix.info/blog/2019/01/creating-a-reproducible-workflow-with-cwl/">
<img src="https://hpc.guix.info/static/images/blog/cwl-provenance-graph.png" /></a>
</p>
<p>
For more see <a href="https://hpc.guix.info/blog/2019/01/creating-a-reproducible-workflow-with-cwl/">Creating a reproducible workflow with CWL</a> by Pjotr Prins.
</p>
</div>
</div>
<div id="outline-container-orgf30b46f" class="outline-2">
<h2 id="orgf30b46f"><span class="section-number-2">5</span> Using the Arvados API</h2>
<div class="outline-text-2" id="text-5">
<p>
Arvados provides a rich API for accessing internals of the Cloud
infrastructure.
</p>
<p>
In above script <code>bh20-seq-analyzer</code> there are examples of querying the
<a href="https://doc.arvados.org/api/index.html">Arvados API</a> using the <a href="https://pypi.org/project/arvados-python-client/">Python Arvados client and libraries</a>. For example
get a list of <a href="https://github.com/arvados/bh20-seq-resource/blob/2baa88b766ec540bd34b96599014dd16e393af39/bh20seqanalyzer/main.py#L228">projects</a> in Arvados. Main thing is to get the
<code>ARVADOS-API-HOST</code> and <code>ARVADOS-API-TOKEN</code> right as is shown above.
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<div id="outline-container-org3af3122" class="outline-2">
<h2 id="org3af3122"><span class="section-number-2">6</span> Troubleshooting</h2>
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<p>
When workflows have errors we should check the logs in Arvados.
</p>
<p>
Go to the <a href="https://workbench.lugli.arvadosapi.com/projects/lugli-j7d0g-825x3r5vcs41dus">project</a> page for 'COVID-19-BH20 Shared Project' -> 'Public
Sequence Resource'. Click on analysis runs
<a href="https://workbench.lugli.arvadosapi.com/projects/lugli-j7d0g-y4k4uswcqi3ku56">https://workbench.lugli.arvadosapi.com/projects/lugli-j7d0g-y4k4uswcqi3ku56</a>
and 'Subprojects'. Click one of the runs and then on 'Processes' and you'll
see what parts failed.
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<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 2020-11-09 Mon 01:20</small>.
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