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<body>
<header>
<nav>
<a href="https://github.com/common-workflow-library/cwl-patterns">CWL Patterns</a>
</nav>
<h1>Rabix</h1>
Power tools for the Common Workflow Language
</header>
<div class="content">
<section>
<h1>What is the Common Workflow Language?</h1>
<p>The Common Workflow Language
(<a href="http://www.commonwl.org/" target="_blank">CWL</a>)
is a widely supported, open source,
vendor neutral specification for workflow descriptions.
Because there are a wide variety of executors that support CWL,
the same CWL document will run on a laptop, on HPC clusters,
on raw cloud infrastructure and on a variety of cloud platforms.
</p>
<p>
See the current list of implementations that support CWL
<a href="https://www.commonwl.org/#Implementations">here</a>.
</p>
<p>
Looking for how to implement something in CWL? This list of
<a href="https://github.com/common-workflow-library/cwl-patterns">CWL Patterns</a> might help.
</p>
</section>
<section>
<h1>What does Rabix provide?</h1>
<section>
<h2>Rabix Benten: Code intelligence for CWL editing</h2>
<p>Benten is a language server for Common Workflow Language documents.
It works with any editor/IDE that has language server support, such
as VS Code, VI, emacs etc.
</p>
<img class="pure-img" src="https://raw.githubusercontent.com/rabix/benten/master/media/2019.12.03/full-window.png">
<nav>
<ul>
<li>
<a href="https://github.com/rabix/benten/releases" target="_blank">
<span><span data-icon="" class="icon"></span>Server releases</span>
</a>
</li>
<li>
<a href="https://marketplace.visualstudio.com/items?itemName=sbg-rabix.benten-cwl" target="_blank">
<span><span data-icon="" class="icon"></span>VS Code extension</span>
</a>
</li>
<li>
<a href="https://github.com/rabix/benten/issues" target="_blank">
<span><span data-icon="" class="icon"></span>Support</span>
</a>
</li>
<li>
<a href="https://github.com/rabix/benten" target="_blank">
<span><span data-icon="" class="icon"></span>Source code</span>
</a>
</li>
</ul>
</nav>
</section>
<section>
<h2>sbpack: Command line interface for pushing and pulling local CWL to/from a Seven Bridges Platform</h2>
<p>sbpack is a command line tool, written in Python, to upload (sbpack)
and download (sbpull) CWL apps to/from any Seven Bridges powered
platform. This enables local text-based CWL development, use of
version control for workflows, and the ability to send workflows to
and from the platform with ease.
</p>
<nav>
<ul>
<li>
<a href="https://pypi.org/project/sbpack/" target="_blank">
<span><span data-icon="" class="icon"></span>Python Package</span>
</a>
</li>
<li>
<a href="https://github.com/rabix/sbpack/issues" target="_blank">
<span><span data-icon="" class="icon"></span>Support</span>
</a>
</li>
<li>
<a href="https://github.com/rabix/sbpack" target="_blank">
<span><span data-icon="" class="icon"></span>Source code</span>
</a>
</li>
</ul>
</nav>
</section>
<section>
<h2>CWL-SVG: interactive SVG visualization of CWL workflows</h2>
<p>
CWL-SVG is a Typescript library for visualization of
Common Workflow Language workflows. It can be easily
integrated into a website or typescript application to show
interactive views of a CWL workflow.
</p>
<p>
CWL-SVG is used in variety of projects including
<a href="https://github.com/BiRG/Omics-Dashboard" target="_blank">
Data Science and Bioinformatics Research Group's Omics Dashboard</a>,
<a href="https://github.com/curoverse/arvados-workbench2" target="_blank">
Arvados workbench</a>,
<a href="https://github.com/TMiguelT/vue-cwl" target="_blank">
Vue CWL</a>,
the <a href="https://scidap.com" target="_blank">
Scientific Data Analysis Platform</a>,
and, of course, in Rabix Composer which is used on the Seven Bridges platform.
</p>
<nav>
<ul>
<li>
<a href="https://www.npmjs.com/package/cwl-svg" target="_blank">
<span><span data-icon="" class="icon"></span>NPM package</span>
</a>
</li>
<li>
<a href="https://github.com/rabix/cwl-svg/issues" target="_blank">
<span><span data-icon="" class="icon"></span>Support</span>
</a>
</li>
<li>
<a href="https://github.com/rabix/cwl-svg" target="_blank">
<span><span data-icon="" class="icon"></span>Source code</span>
</a>
</li>
</ul>
</nav>
</section>
<section>
<h2>CWL-TS: Typescript data model for Common Workflow Language</h2>
<p>
CWL-ts is a data model library for CWL made for use in TypeScript
and JavaScript (primarily client-side) applications.
It supports JSON schemas and mappings for draft-3, draft-4, and v1.0.
Draft-2 support is SevenBridges flavored.
</p>
<nav>
<ul>
<li>
<a href="https://www.npmjs.com/package/cwlts" target="_blank">
<span><span data-icon="" class="icon"></span>NPM package</span>
</a>
</li>
<li>
<a href="https://github.com/rabix/cwl-ts/issues" target="_blank">
<span><span data-icon="" class="icon"></span>Support</span>
</a>
</li>
<li>
<a href="https://github.com/rabix/cwl-ts" target="_blank">
<span><span data-icon="" class="icon"></span>Source code</span>
</a>
</li>
</ul>
</nav>
</section>
<section>
<h2>Rabix Composer: Visual programming in CWL [Legacy]</h2>
<p>CWL documents are text files describing computational steps.
CWL written in YAML format is compact and easily read by users.
While some users are comfortable creating CWL workflows "by
hand" using a text editor, others may prefer Rabix Composer:
a powerful, open source, graphical editor allowing
visual programming in CWL. Rabix Composer enables a user to
quickly create complex CWL workflows without having to
remember the details of CWL syntax.
</p>
<h3>Support Notice</h3>
<p><em>
Rabix Composer will remain available as a local sbg:draft2 and
CWL 1.0 tool and workflow editor. However, please note that Seven
Bridges is not actively maintaining or extending Rabix Composer at
the moment (Q2 2021). The repository will remain open for new issues
and pull requests, but please have in mind that those may not be
processed in a timely manner.
</p>
<p>
If you need an up-to-date CWL editor, you can create an account
either on the
<a href="http://cgc.sbgenomics.com/", target="_blank">CGC</a>,
<a href="https://platform.sb.biodatacatalyst.nhlbi.nih.gov/", target="_blank">Biodata Catalyst powered by Seven Bridges</a>,
or on <a href="https://cavatica.sbgenomics.com/", target="_blank">CAVATICA</a>
and use the Web Composer available there. Web Composer is also
available on the Seven Bridges Commercial offerings.
</em></p>
<img class="pure-img" src="https://github.com/rabix/composer/raw/master/doc/images/workflows.gif">
<nav>
<ul>
<li>
<a href="http://docs.rabix.io/rabix-composer-home" target="_blank">
<span><span data-icon="" class="icon"></span>Documentation</span>
</a>
</li>
<li>
<a href="https://github.com/rabix/composer/issues" target="_blank">
<span><span data-icon="" class="icon"></span>Support</span>
</a>
</li>
<li>
<a href="https://github.com/rabix/composer" target="_blank">
<span><span data-icon="" class="icon"></span>Source code</span>
</a>
</li>
</ul>
</nav>
<nav>
<ul>
<li class="button button-pill">
<a href="https://github.com/rabix/composer/releases/download/1.0.1/rabix-composer-1.0.1.dmg">
<span><span data-icon="" class="icon"></span>Mac</span>
</a>
</li>
<li class="button button-pill">
<a href="https://github.com/rabix/composer/releases/download/1.0.1/rabix-composer-1.0.1-x86_64.AppImage">
<span><span data-icon="" class="icon"></span>Linux</span>
</a>
</li>
<li class="button button-pill">
<a href="https://github.com/rabix/composer/releases/download/1.0.1/rabix-composer.Setup.1.0.1.exe">
<span><span data-icon="" class="icon"></span>Windows</span>
</a>
</li>
</ul>
</nav>
</section>
<section>
<h2>Rabix Executor: Runner for CWL pipelines [Legacy]</h2>
<p>
Rabix Executor is a workflow runner that can execute
CWL sbg:draft2 and CWL 1.0 pipelines. It has support for the
TES API and can be used in a limited manner to run pipelines
on cloud infrastructure.
[<a href="https://www.ncbi.nlm.nih.gov/pubmed/27896971" target="_blank">PubMed</a>,
<a href="http://biorxiv.org/content/early/2016/10/23/074708" target="_blank">bioRxiv</a>]
</p>
<p>
When the Rabix project was in it's infancy and the CWL specification
was just being developed (ca. 2014-2016) Rabix Executor was
the only executor capable of running CWL. It proved invaluable
as a test bed for ideas for the specification that evolved into
CWL and as a living implementation of the specification.
</p>
<p><em>
There are now many modern
<a href="https://www.commonwl.org/#Implementations">CWL executors</a>
for every conceivable platform. Rabix Executor is now in maintenance mode.
Rabix Executor remains a stable local test runner for those people
wishing to run sbg:draft2 pipelines locally, but no new features will be added to it.
</em></p>
<nav>
<ul>
<li>
<a href="https://github.com/rabix/bunny/releases" target="_blank">
<span><span data-icon="" class="icon"></span>Releases</span>
</a>
</li>
<li>
<a href="https://github.com/rabix/bunny/issues" target="_blank">
<span><span data-icon="" class="icon"></span>Support</span>
</a>
</li>
<li>
<a href="https://github.com/rabix/bunny" target="_blank">
<span><span data-icon="" class="icon"></span>Source code</span>
</a>
</li>
</ul>
</nav>
</section>
</section>
<hr>
<section id="faq" class="section-a">
<h1>With love from Seven Bridges</h1>
<p>Seven Bridges is passionate about open standards in science and about
providing high quality open source developer tooling around those standards.
Rabix (a portmanteau of "Reproducible Analyses for Bioinformatics") was founded by
<a href="https://www.sevenbridges.com" target="_blank">SevenBridges</a> in 2015
to support this mission. The Rabix team plays a key role in developing CWL
and tooling around CWL.
</p>
<nav>
<ul>
<li>
<a href="mailto:[email protected]" target="_blank">
<span data-icon="" class="icon"></span>[email protected]</a>
</li>
<li>
<a href="https://github.com/rabix" target="_blank">
<span><span data-icon="" class="icon"></span>github</span>
</a>
</li>
</ul>
</nav>
</section>
</div>
<footer>
<p>
Rabix is a Trademark of <a href="https://www.sevenbridges.com" target="_blank">Seven Bridges</a>
</p>
<p>
Copyright © 2019 Seven Bridges
</p>
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