exclude: ["Rakefile", "tmp", "vendor"]
navbar:
+ start:
+ - Getting Started:
+ - start/index.html.textile.liquid
+ - Quickstart:
+ - start/getting_started/firstpipeline.html.textile.liquid
+ - Simple Use Cases:
+ - start/getting_started/sharedata.html.textile.liquid
+
userguide:
- Getting Started:
- user/index.html.textile.liquid
</div>
<div class="collapse navbar-collapse" id="bs-navbar-collapse">
<ul class="nav navbar-nav">
+ <li {% if page.navsection == 'start' %} class="active" {% endif %}><a href="{{ site.baseurl }}/start/index.html">Getting Started</a></li>
<li {% if page.navsection == 'userguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/user/index.html">User Guide</a></li>
<li {% if page.navsection == 'sdk' %} class="active" {% endif %}><a href="{{ site.baseurl }}/sdk/index.html">SDK Reference</a></li>
<li {% if page.navsection == 'api' %} class="active" {% endif %}><a href="{{ site.baseurl }}/api/index.html">API Reference</a></li>
<link href="{{ site.baseurl }}/css/badges.css" rel="stylesheet">
<link href="{{ site.baseurl }}/css/code.css" rel="stylesheet">
<link href="{{ site.baseurl }}/css/font-awesome.css" rel="stylesheet">
+ <link href="{{ site.baseurl }}/css/carousel-override.css" rel="stylesheet">
<style>
html {
height:100%;
--- /dev/null
+.carousel-control {
+ width: 5%;
+}
+
+.carousel-caption {
+ position: static;
+ background: rgba(0,0,0,0.6);
+ color: white;
+ padding-bottom: 35px;
+ padding-left: 1em;
+ padding-right: 1em;
+ padding-top: 15px;
+}
+
+.carousel {
+ overflow: hidden;
+ border-radius: 5px;
+ max-width: 900px;
+ margin: 1em;
+}
+
+.carousel-indicators {
+ bottom: 0px;
+}
+
<div class="row">
<div class="col-sm-6">
<h1>ARVADOS</h1>
- <p>manuals, guides, and references</p>
+ <p>A free and open source bioinformatics platform for genomic and biomedical data</p>
</div>
<div class="col-sm-6">
<img src="images/dax-reading-book.png" style="max-height: 10em" alt="Dax reading a book" />
<div class="container-fluid">
<div class="row">
<div class="col-sm-5">
- <p>This site contains documentation for the <a href="https://arvados.org/">Arvados platform</a>. The documentation is being developed as part of the open source project. It is a work in progress that has just gotten started. You can get involved by <a href="https://arvados.org/projects/arvados/wiki/Documentation">joining the documentation effort</a>.
+ <p><a href="https://arvados.org/">Arvados</a> enables you to quickly begin using cloud computing resources in your bioinformatics work. It allows you to track and your methods and datasets, share them securely, and easily re-run analyses.
+ </p>
+ <p>Check out our <a href="{{ site.baseurl }}/start/index.html">key features</a>, complete with screenshots, and then follow our tutorial to <a href="{{ site.baseurl }}/start/getting_started/firstpipeline.html">run your first pipeline</a> using our <a href="http://lp.curoverse.com/beta-signup/">public beta</a>.
+ </p>
+ <p>On this page, you can also find more in-depth guides for using Arvados.
+ </p>
</div>
<div class="col-sm-7" style="border-left: solid; border-width: 1px">
+ <p>
+ <a href="{{ site.baseurl }}/start/index.html">Getting Started</a> — Start here if you're new to Arvados.
+ </p>
<p>
<a href="{{ site.baseurl }}/user/index.html">User Guide</a> — How to manage data and do analysis with Arvados.
</p>
--- /dev/null
+---
+layout: default
+navsection: start
+title: Run your first pipeline in minutes
+...
+
+h2. LobSTR v3
+
+In this quickstart guide, we'll run an existing pipeline with pre-existing data. Step-by-step instructions are shown below. You can follow along using your own local install or by using Curoverse's <a href="http://lp.curoverse.com/beta-signup/">hosted version of Arvados</a> (in public beta, any Google account can be used to login).
+
+(For more information about this pipeline, see our <a href="https://arvados.org/projects/arvados/wiki/LobSTR_tutorial">detailed lobSTR guide</a>).
+
+<div id="carousel-firstpipe" class="carousel slide">
+ <!-- Indicators -->
+ <ol class="carousel-indicators">
+ <li data-target="#carousel-firstpipe" data-slide-to="0" class="active"></li>
+ <li data-target="#carousel-firstpipe" data-slide-to="1"></li>
+ <li data-target="#carousel-firstpipe" data-slide-to="2"></li>
+ <li data-target="#carousel-firstpipe" data-slide-to="3"></li>
+ <li data-target="#carousel-firstpipe" data-slide-to="4"></li>
+ <li data-target="#carousel-firstpipe" data-slide-to="5"></li>
+ <li data-target="#carousel-firstpipe" data-slide-to="6"></li>
+ </ol>
+
+ <!-- Wrapper for slides -->
+ <div class="carousel-inner" role="listbox">
+ <div class="item active">
+ <img src="{{ site.baseurl }}/images/quickstart/1.png" alt="Step 1. At the dashboard, click 'Run a pipeline...'.">
+ <div class="carousel-caption">
+ Step 1. At the dashboard, click 'Run a pipeline...'.
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/quickstart/2.png" alt="Choose 'lobstr v.3' and hit 'Next'.">
+ <div class="carousel-caption">
+ Choose 'lobstr v.3' and hit 'Next'.
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/quickstart/3.png" alt="Rename the pipeline intance, then click 'Run'. Alternatively, choose new inputs.">
+ <div class="carousel-caption">
+ Rename the pipeline intance, then click 'Run'. Alternatively, choose new inputs.
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/quickstart/4.png" alt="Here we search for and choose new inputs.">
+ <div class="carousel-caption">
+ Here we search for and choose new inputs.
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/quickstart/5.png" alt="After the job completes, you can re-run it with one click.">
+ <div class="carousel-caption">
+ After the job completes, you can re-run it with one click.
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/quickstart/6.png" alt="You can inspect details about the pipeline which are automatically logged.">
+ <div class="carousel-caption">
+ You can inspect automatically-logged details about the pipeline.
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/quickstart/7.png" alt="Click 'Create sharing link' to share with people outside Arvados. [END]">
+ <div class="carousel-caption">
+ Click 'Create sharing link' to share with people outside Arvados. [END]
+ </div>
+ </div>
+
+ </div>
+
+ <!-- Controls -->
+ <a class="left carousel-control" href="#carousel-firstpipe" role="button" data-slide="prev">
+ <span class="glyphicon glyphicon-chevron-left" aria-hidden="true"></span>
+ <span class="sr-only">Previous</span>
+ </a>
+ <a class="right carousel-control" href="#carousel-firstpipe" role="button" data-slide="next">
+ <span class="glyphicon glyphicon-chevron-right" aria-hidden="true"></span>
+ <span class="sr-only">Next</span>
+ </a>
+</div>
+
+Tip: You may need to make your browser window bigger to see full-size images in the gallery above.
--- /dev/null
+---
+layout: default
+navsection: start
+title: "Key Features"
+...
+
+h2. Key Features
+
+<ul>
+<li><strong>Track your methods</strong><br/>
+We log every compute job: software versions, machine images, input and output data hashes. Rely on a computer, not your memory and your note-taking skills.</li>
+<li><strong>Share your methods</strong><br/>
+Show other people what you did. Let them use your workflow on their own data. Publish a permalink to your methods and data, so others can reproduce and build on them easily.</li>
+<li><strong>Track data origin</strong><br/>
+Did you really only use fully consented public data in this analysis?</li>
+<li><strong>Get results sooner</strong><br/>
+Run your compute jobs faster by using multi-nodes and multi-cores, even if your programs are single-threaded.</li>
+</ul>
+
+Check out the gallery below, which shows highlights of key features of Workbench, the web interface to Arvados.
+
+h3. Take a look (Screenshots gallery)
+
+<div id="carousel-keyfeatures" class="carousel slide">
+ <!-- Indicators -->
+ <ol class="carousel-indicators">
+ <li data-target="#carousel-keyfeatures" data-slide-to="0" class="active"></li>
+ <li data-target="#carousel-keyfeatures" data-slide-to="1"></li>
+ <li data-target="#carousel-keyfeatures" data-slide-to="2"></li>
+ <li data-target="#carousel-keyfeatures" data-slide-to="3"></li>
+ <li data-target="#carousel-keyfeatures" data-slide-to="4"></li>
+ <li data-target="#carousel-keyfeatures" data-slide-to="5"></li>
+ <li data-target="#carousel-keyfeatures" data-slide-to="6"></li>
+ <li data-target="#carousel-keyfeatures" data-slide-to="7"></li>
+ <li data-target="#carousel-keyfeatures" data-slide-to="8"></li>
+ </ol>
+
+ <!-- Wrapper for slides -->
+ <div class="carousel-inner" role="listbox">
+ <div class="item active">
+ <img src="{{ site.baseurl }}/images/keyfeatures/dashboard2.png" alt="[START] After logging in, you see Workbench's dashboard.">
+ <div class="carousel-caption">
+ [START] After logging in, you see Workbench's dashboard.
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/keyfeatures/running2.png" alt="Pipelines describe a set of computational tasks (jobs).">
+ <div class="carousel-caption">
+ Pipelines describe a set of computational tasks (jobs).
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/keyfeatures/log.png" alt="The output of all jobs is logged and stored automatically.">
+ <div class="carousel-caption">
+ The output of all jobs is logged and stored automatically.
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/keyfeatures/graph.png" alt="Pipelines can be also viewed in auto-generated graph form.">
+ <div class="carousel-caption">
+ Pipelines can be also viewed in auto-generated graph form.
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/keyfeatures/rerun.png" alt="Pipelines can easily be re-run...">
+ <div class="carousel-caption">
+ Pipelines can easily be re-run...
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/keyfeatures/chooseinputs.png" alt="...by changing parameters or picking new datasets...">
+ <div class="carousel-caption">
+ ...by changing parameters or picking new datasets...
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/keyfeatures/webupload.png" alt="...which can be uploaded right in Workbench.">
+ <div class="carousel-caption">
+ ...which can be uploaded right in Workbench.
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/keyfeatures/collectionpage.png" alt="Collections allow sharing datasets and job outputs easily.">
+ <div class="carousel-caption">
+ Collections allow sharing datasets and job outputs easily.
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/keyfeatures/provenance.png" alt="Data provenance is tracked automatically. [END]">
+ <div class="carousel-caption">
+ Data provenance is tracked automatically. [END]
+ </div>
+ </div>
+
+
+ </div>
+
+ <!-- Controls -->
+ <a class="left carousel-control" href="#carousel-keyfeatures" role="button" data-slide="prev">
+ <span class="glyphicon glyphicon-chevron-left" aria-hidden="true"></span>
+ <span class="sr-only">Previous</span>
+ </a>
+ <a class="right carousel-control" href="#carousel-keyfeatures" role="button" data-slide="next">
+ <span class="glyphicon glyphicon-chevron-right" aria-hidden="true"></span>
+ <span class="sr-only">Next</span>
+ </a>
+</div>
--- /dev/null
+---
+layout: default
+navsection: start
+title: Sharing Data
+...
+
+You can easily share data entirely through Workbench, the web interface to Arvados.
+
+h2. Upload and share your existing data
+
+Step-by-step instructions are shown below.
+
+<div id="carousel-sharedata" class="carousel slide">
+ <!-- Indicators -->
+ <ol class="carousel-indicators">
+ <li data-target="#carousel-sharedata" data-slide-to="0" class="active"></li>
+ <li data-target="#carousel-sharedata" data-slide-to="1"></li>
+ <li data-target="#carousel-sharedata" data-slide-to="2"></li>
+ <li data-target="#carousel-sharedata" data-slide-to="3"></li>
+ <li data-target="#carousel-sharedata" data-slide-to="4"></li>
+ <li data-target="#carousel-sharedata" data-slide-to="5"></li>
+ <li data-target="#carousel-sharedata" data-slide-to="6"></li>
+ <li data-target="#carousel-sharedata" data-slide-to="7"></li>
+ </ol>
+
+ <!-- Wrapper for slides -->
+ <div class="carousel-inner" role="listbox">
+ <div class="item active">
+ <img src="{{ site.baseurl }}/images/uses/gotohome.png" alt="Step 1. From the dashboard, go to your Home project.">
+ <div class="carousel-caption">
+ Step 1. From the dashboard, go to your Home project.
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/uses/uploaddata.png" alt="Add data - Upload files.">
+ <div class="carousel-caption">
+ Add data - Upload files.
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/uses/choosefiles.png" alt="A new collection is created automatically. Choose files to upload and hit Start.">
+ <div class="carousel-caption">
+ A new collection is created automatically. Choose files to upload and hit Start.
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/uses/uploading.png" alt="Files will upload and stay uploaded even if the browser is closed.">
+ <div class="carousel-caption">
+ Files will upload and stay uploaded even if the browser is closed.
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/uses/rename.png" alt="Rename the collection appropriately.">
+ <div class="carousel-caption">
+ Rename the collection appropriately.
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/uses/share.png" alt="Click 'Create sharing link'. You can click 'unshare' at any later point.">
+ <div class="carousel-caption">
+ Click 'Create sharing link'. You can click 'unshare' at any later point.
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/uses/shared.png" alt="Now just share this link with anyone you want.">
+ <div class="carousel-caption">
+ Now just share this link with anyone you want.
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/uses/sharedsubdirs.png" alt="Here's a more complex collection. [END]">
+ <div class="carousel-caption">
+ Here's a more complex collection. [END]
+ </div>
+ </div>
+
+ </div>
+
+ <!-- Controls -->
+ <a class="left carousel-control" href="#carousel-sharedata" role="button" data-slide="prev">
+ <span class="glyphicon glyphicon-chevron-left" aria-hidden="true"></span>
+ <span class="sr-only">Previous</span>
+ </a>
+ <a class="right carousel-control" href="#carousel-sharedata" role="button" data-slide="next">
+ <span class="glyphicon glyphicon-chevron-right" aria-hidden="true"></span>
+ <span class="sr-only">Next</span>
+ </a>
+</div>
+
+Tip: You may need to make your browser window bigger to see full-size images in the gallery above.
--- /dev/null
+---
+layout: default
+navsection: start
+title: Welcome to Arvados!
+...
+
+This guide provides an introduction to using Arvados to solve big data bioinformatics problems.
+
+h2. What is Arvados?
+
+Arvados is a free and open source bioinformatics platform for genomic and biomedical data.
+
+We address the needs of IT directors, lab principals, and bioinformaticians.
+
+h2. Why use Arvados?
+
+Arvados enables you to quickly begin using cloud computing resources in your bioinformatics work. It allows you to track and your methods and datasets, share them securely, and easily re-run analyses.
+
+h3. Take a look (Screenshots gallery)
+
+<div id="carousel-keyfeatures" class="carousel slide">
+ <!-- Indicators -->
+ <ol class="carousel-indicators">
+ <li data-target="#carousel-keyfeatures" data-slide-to="0" class="active"></li>
+ <li data-target="#carousel-keyfeatures" data-slide-to="1"></li>
+ <li data-target="#carousel-keyfeatures" data-slide-to="2"></li>
+ <li data-target="#carousel-keyfeatures" data-slide-to="3"></li>
+ <li data-target="#carousel-keyfeatures" data-slide-to="4"></li>
+ <li data-target="#carousel-keyfeatures" data-slide-to="5"></li>
+ <li data-target="#carousel-keyfeatures" data-slide-to="6"></li>
+ <li data-target="#carousel-keyfeatures" data-slide-to="7"></li>
+ <li data-target="#carousel-keyfeatures" data-slide-to="8"></li>
+ </ol>
+
+ <!-- Wrapper for slides -->
+ <div class="carousel-inner" role="listbox">
+ <div class="item active">
+ <img src="{{ site.baseurl }}/images/keyfeatures/dashboard2.png" alt="[START] After logging in, you see Workbench's dashboard.">
+ <div class="carousel-caption">
+ [START] After logging in, you see Workbench's dashboard.
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/keyfeatures/running2.png" alt="Pipelines describe a set of computational tasks (jobs).">
+ <div class="carousel-caption">
+ Pipelines describe a set of computational tasks (jobs).
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/keyfeatures/log.png" alt="The output of all jobs is logged and stored automatically.">
+ <div class="carousel-caption">
+ The output of all jobs is logged and stored automatically.
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/keyfeatures/graph.png" alt="Pipelines can be also viewed in auto-generated graph form.">
+ <div class="carousel-caption">
+ Pipelines can be also viewed in auto-generated graph form.
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/keyfeatures/rerun.png" alt="Pipelines can easily be re-run...">
+ <div class="carousel-caption">
+ Pipelines can easily be re-run...
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/keyfeatures/chooseinputs.png" alt="...by changing parameters or picking new datasets...">
+ <div class="carousel-caption">
+ ...by changing parameters or picking new datasets...
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/keyfeatures/webupload.png" alt="...which can be uploaded right in Workbench.">
+ <div class="carousel-caption">
+ ...which can be uploaded right in Workbench.
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/keyfeatures/collectionpage.png" alt="Collections allow sharing datasets and job outputs easily.">
+ <div class="carousel-caption">
+ Collections allow sharing datasets and job outputs easily.
+ </div>
+ </div>
+
+ <div class="item">
+ <img src="{{ site.baseurl }}/images/keyfeatures/provenance.png" alt="Data provenance is tracked automatically. [END]">
+ <div class="carousel-caption">
+ Data provenance is tracked automatically. [END]
+ </div>
+ </div>
+
+
+ </div>
+
+ <!-- Controls -->
+ <a class="left carousel-control" href="#carousel-keyfeatures" role="button" data-slide="prev">
+ <span class="glyphicon glyphicon-chevron-left" aria-hidden="true"></span>
+ <span class="sr-only">Previous</span>
+ </a>
+ <a class="right carousel-control" href="#carousel-keyfeatures" role="button" data-slide="next">
+ <span class="glyphicon glyphicon-chevron-right" aria-hidden="true"></span>
+ <span class="sr-only">Next</span>
+ </a>
+</div>
+
+Tip: You may need to make your browser window bigger to see full-size images in the gallery above.
+
+h3. Key Features
+
+<ul>
+<li><strong>Track your methods</strong><br/>
+We log every compute job: software versions, machine images, input and output data hashes. Rely on a computer, not your memory and your note-taking skills.</li>
+<li><strong>Share your methods</strong><br/>
+Show other people what you did. Let them use your workflow on their own data. Publish a permalink to your methods and data, so others can reproduce and build on them easily.</li>
+<li><strong>Track data origin</strong><br/>
+Did you really only use fully consented public data in this analysis?</li>
+<li><strong>Get results sooner</strong><br/>
+Run your compute jobs faster by using multi-nodes and multi-cores, even if your programs are single-threaded.</li>
+</ul>
--- /dev/null
+---
+layout: default
+navsection: start
+title: Welcome to Arvados!
+...
+
+This guide provides an introduction to using Arvados to solve big data bioinformatics problems.
+
+
+h2. Typographic conventions
+
+This manual uses the following typographic conventions:
+
+<notextile>
+<ul>
+<li>Code blocks which are set aside from the text indicate user input to the system. Commands that should be entered into a Unix shell are indicated by the directory where you should enter the command ('~' indicates your home directory) followed by '$', followed by the highlighted <span class="userinput">command to enter</span> (do not enter the '$'), and possibly followed by example command output in black. For example, the following block indicates that you should type <code>ls foo.*</code> while in your home directory and the expected output will be "foo.input" and "foo.output".
+</notextile>
+
+<div class="custom-container key-features">
+<a class="prev" href="#">‹</a>
+
+<div class="carousel">
+ <ul>
+ <li><img class="hascaption" src="{{ site.baseurl }}/images/keyfeatures/dashboard2.png" style="width:909px; height:503px;" title="[START] After logging in, you see Workbench's dashboard."></li>
+ <li><img class="hascaption" src="{{ site.baseurl }}/images/keyfeatures/running2.png" style="width:909px; height:503px;" title="Pipelines describe a set of computational tasks (jobs)."></li>
+ <li><img class="hascaption" src="{{ site.baseurl }}/images/keyfeatures/log.png" style="width:909px; height:503px;" title="The output of all jobs is logged and stored automatically."></li>
+ <li><img class="hascaption" src="{{ site.baseurl }}/images/keyfeatures/graph.png" style="width:909px; height:503px;" title="Pipelines can be also viewed in auto-generated graph form."></li>
+ <li><img class="hascaption" src="{{ site.baseurl }}/images/keyfeatures/rerun.png" style="width:909px; height:503px;" title="Pipelines can easily be re-run..."></li>
+ <li><img class="hascaption" src="{{ site.baseurl }}/images/keyfeatures/chooseinputs.png" style="width:909px; height:503px;" title="...by changing parameters or picking new datasets..."></li>
+ <li><img class="hascaption" src="{{ site.baseurl }}/images/keyfeatures/webupload.png" style="width:909px; height:503px;" title="...which can be uploaded right in Workbench."></li>
+ <li><img class="hascaption" src="{{ site.baseurl }}/images/keyfeatures/collectionpage.png" style="width:909px; height:503px;" title="Collections allow sharing datasets and job outputs easily."></li>
+ <li><img class="hascaption" src="{{ site.baseurl }}/images/keyfeatures/provenance.png" style="width:909px; height:503px;" title="Data provenance is tracked automatically. [END]"></li>
+ </ul>
+</div>
+<a class="next" href="#">›</a>
+<div class="clear"></div>
+</div>
+
+<script type="text/javascript">
+(function() {
+ $(".key-features .carousel").jCarouselLite({
+ btnNext: ".key-features .next",
+ btnPrev: ".key-features .prev",
+ visible: 1,
+ });
+});
+('.hascaption').each(function() {
+ $(this).after( "<div style='background: rgba(0,0,0,0.6); color: white; padding: 1.4em;'>" + $(this).attr('title') + "</div>" );
+});
+</script>