Galaxy Interactive Tools

name: inverse
layout: true
class: center, middle, inverse

</span></div>

</span></div>

---

# Galaxy Interactive Tools

<div class="contributors-line">
		
	
<ul class="text-list">
			
			<li>
				<a href="/training-material/hall-of-fame/natefoo/" class="contributor-badge contributor-natefoo"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/natefoo?s=36" alt="Nate Coraor avatar" width="36" class="avatar" />
    Nate Coraor</a>
			<li>
				<a href="/training-material/hall-of-fame/eancelet/" class="contributor-badge contributor-eancelet"><img src="https://avatars.githubusercontent.com/eancelet?s=36" alt="Estelle Ancelet avatar" width="36" class="avatar" />
    Estelle Ancelet</a>
			<li>
				<a href="/training-material/hall-of-fame/abretaud/" class="contributor-badge contributor-abretaud"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/abretaud?s=36" alt="Anthony Bretaudeau avatar" width="36" class="avatar" />
    Anthony Bretaudeau</a></li>
</ul>

</div>

<div class="footnote" style="bottom: 8em;">
  <i class="far fa-calendar" aria-hidden="true"></i><span class="visually-hidden">last_modification</span> Updated:   
  <i class="fas fa-fingerprint" aria-hidden="true"></i><span class="visually-hidden">purl</span><abbr title="Persistent URL">PURL</abbr>: <a href="https://gxy.io/GTN:S00014">gxy.io/GTN:S00014</a>
</div>

<div class="footnote" style="bottom: 5em;">

<i class="far fa-play-circle" aria-hidden="true"></i><span class="visually-hidden">video-slides</span> <a href="/training-material/videos/watch.html?v=/admin/tutorials/interactive-tools/slides">Video slides</a> |

<i class="fas fa-file-alt" aria-hidden="true"></i><span class="visually-hidden">text-document</span><a href="slides-plain.html"> Plain-text slides</a> |

</div>

<div class="footnote" style="bottom: 2em;">
    <strong>Tip: </strong>press <kbd>P</kbd> to view the presenter notes
    | <i class="fa fa-arrows" aria-hidden="true"></i><span class="visually-hidden">arrow-keys</span> Use arrow keys to move between slides

</div>

???
Presenter notes contain extra information which might be useful if you intend to use these slides for teaching.

Press `P` again to switch presenter notes off

Press `C` to create a new window where the same presentation will be displayed.
This window is linked to the main window. Changing slides on one will cause the
slide to change on the other.

Useful when presenting.

---

### <i class="fas fa-bullseye" aria-hidden="true"></i><span class="visually-hidden">objectives</span> Objectives

- Learn the differences between Galaxy Interactive Environments and Galaxy Interactive Tools

- Have an understanding of what Galaxy Interactive Tools are and how they work

---

# History

## 2015

@hexylena, @bgruening, and @jmchilton create Galaxy Interactive Environments (GIEs)

GIEs use Galaxy's *visualization framework* to run certain types of *interactive* visualizations (e.g. Jupyter Notebook)

GIEs run in a docker container on the Galaxy server or a single remote Docker server

???

- Galaxy Interactive Environments were added to Galaxy in 2015.
- They are a type of visualization in Galaxy.
- Accessible through the “Visualize” menu or under the visualization button on a dataset with a specific datatype.
- Back then, the docker container serving an interactive environment could not be run on a cluster.
- More details within Galaxy Interactive Environment slides.

---
# History

## 2016

Support for Docker Swarm is added, allowing running a cluster for GIEs

???

- As of 2016, Docker includes swarm mode for natively managing a cluster of Docker Engines called a swarm.
- This allowed to run Galaxy Interactive Environment on a cluster.

---
# History

## 2019

@blankenberg creates Galaxy Interactive Tools (GxITs)

Building on the GIE concept, but run as *tools*

Tools run just as any other Galaxy job (e.g. via Slurm, HTCondor)

You will sometimes see Interactive Tools referred to as Interactive Environments version 2

???

- In 2019, were created the Galaxy Interactive Tools.
- Like interactive environment, Galaxy Interactive Tools are built on docker containers and are accessible through the Galaxy interface.
- But they are considered as tools.
- They are launchable from the toolbox menu, on a predefined destination and prioritized as any other job.

---
# Tool config syntax

```xml
<tool id="interactive_tool_jupyter_notebook" tool_type="interactive" name="Interactive Jupyter Notebook" version="0.1">
    <requirements>
        <container type="docker">quay.io/bgruening/docker-jupyter-notebook:ie2</container>
    </requirements>
    <entry_points>
        <entry_point name="Jupyter Interactive Tool" requires_domain="True">
            <port>8888</port>
            <url>ipython/lab</url>
        </entry_point>
    </entry_points>
</tool>
```

???

- Some settings are needed to configure an interactive tool wrapper.
- The tool type must be set to interactive.
- As a requirement, set the path to the repository where the container is to be pulled from.
- The tool entry point on the container must be defined.
- For instance, for a Jupyter Notebook, you'll give the port the application is served on and the domain name suffix.

---
# Mapping clients to containers

- GIEs: Unique path, e.g. `https://galaxy.example.org/gie-proxy/jupyter/...`
  - Pros: Works with existing SSL certificate
  - Cons: Requires Galaxy session cookie (no sharing), can only run one at a time, closing your browser loses your session
- GxITs: Unique hostname, e.g. `https://<unique-id>.ep.interactivetool.galaxy.example.org/`
  - Pros: Needs no special credentials (can be shared)
  - Cons: Requires *wildcard* DNS entry and *wildcard* SSL certificate (not possible at many sites)

???

- Diverse infrastructures behind Galaxy Interactive Environments and Galaxy Interactive Tools induces various constraints and benefits.
- Particularly in building the path between the browser and the container.

---
# Anatomy of a running Interactive Tool

![Galaxy Interactive Tools Proxy Diagram](../../images/interactive-tools/gxit-proxy-diagram.png "Galaxy Interactive Tools Proxy Diagram")

.reduce70[.footnote[The source for this figure can be found at: https://docs.google.com/presentation/d/1_4PtfM6A4mOxOlgGh6OGWvzFcxD1bdw4CydEWtm5n8k/]]

???

- This slide illustrates the steps allowing a client to interact with a Galaxy Interactive Tool.
- We consider a Galaxy server running behind a reverse proxy (NGINX).
- The client only ever speaks to NGINX on the Galaxy server, running on the standard HTTPS 443 port.
- Based on the elements provided by the URL, NGINX redirects the requests to Galaxy over a unix domain socket as usual.
- On the other hand, HTTP requests targetting interactive tools are redirected by NGINX to a proxy, called GIE Proxy, running on port 8000.
- At this point, remember, when an docker container starts, it will be assigned a host (server or node) and a random port on that host (in our example, port 32768).
- This information is stored by Galaxy in a sqlite database.
- So the GIE proxy checks in this sqlite database to know which node and port the IT container is to be found.
- The GIE proxy forwards the HTTP request to Docker on that node and port.
- Docker, in turn, forwards it to the application (e.g. Jupyter) on the container's port, defined in the wrapper.

---
# Galaxy configuration

Enable docker on a destination in `job_conf.xml` and assign your GxITs to that destination

.left[Set in `galaxy.yml`:]
```yaml
interactivetools_enable: true
interactivetools_map: /srv/galaxy/var/gie-proxy-sessions.sqlite
```

???

- A few settings are needed to get interactive tools running within your Galaxy instance.
- In your galaxy configuration file, enable the use of interactive tools then set the path to the sqlite database storing the proxying data.
- In the job configuration file, give to the tool a destination allowing the use of Docker (more details in the tutorial).

---
# Proxy configuration

Use the proxy configuration that ships with Galaxy

Or the [Node.js-based proxy][usegalaxy_eu-gie_proxy]

[usegalaxy_eu-gie_proxy]: https://galaxy.ansible.com/usegalaxy_eu/gie_proxy

???

- In production, you are likely to use the Node.js based proxy, set up by the Galaxy admin team.
- During developement, you can use the proxy configuration used by default by Galaxy.

---
# Security

The default docker-enabled container exposes all datasets to the tool

Normally this isn't bad (normal tools can't be controlled by the user)

Interactive tools are fully user controllable

Solution: [Embedded Pulsar][job-conf-pulsar-embedded]

[job-conf-pulsar-embedded]: https://github.com/galaxyproject/galaxy/blob/6622ad1acb91866febb3d2f229de7cfb8af3a9f6/lib/galaxy/config/sample/job_conf.xml.sample_advanced#L106

???

- As we have seen, interactive tools are launched in docker containers.
- By default in galaxy, each container has full access to all user's data.
- This is a security issue since a user could take control of an interactive tool and read, write or delete those data.

---
# Embedded Pulsar

Runs a [Pulsar][pulsar] server within the Galaxy application to "stage" (i.e. copy) inputs.

- Pros: Inputs in isolated dir so only that dir is mounted in the container: secure
- Cons: Has to copy inputs on each Interactive Tool execution: slow

[pulsar]: https://github.com/galaxyproject/pulsar

???

- A solution to this security issue is to use embedded pulsar.
- This way, pulsar makes available only the job input data to the container.
- Moreover, these data are read only.
- You will have more details in the tutorial.

---

## Thank You!

This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://training.galaxyproject.org) and all the contributors!

<div class="contributors-line">
		
<table class="contributions">
	
	<tr>
		<td><abbr title="These people wrote the bulk of the tutorial, they may have done the analysis, built the workflow, and wrote the text themselves.">Author(s)</abbr></td>
		<td>
			<a href="/training-material/hall-of-fame/natefoo/" class="contributor-badge contributor-natefoo"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/natefoo?s=36" alt="Nate Coraor avatar" width="36" class="avatar" />
    Nate Coraor</a><a href="/training-material/hall-of-fame/eancelet/" class="contributor-badge contributor-eancelet"><img src="https://avatars.githubusercontent.com/eancelet?s=36" alt="Estelle Ancelet avatar" width="36" class="avatar" />
    Estelle Ancelet</a><a href="/training-material/hall-of-fame/abretaud/" class="contributor-badge contributor-abretaud"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/abretaud?s=36" alt="Anthony Bretaudeau avatar" width="36" class="avatar" />
    Anthony Bretaudeau</a>
		</td>
	</tr>

<tr class="reviewers">
		<td><abbr title="These people reviewed this material for accuracy and correctness">Reviewers</abbr></td>
		<td>
			<a href="/training-material/hall-of-fame/bgruening/" class="contributor-badge contributor-badge-small contributor-bgruening"><img src="https://avatars.githubusercontent.com/bgruening?s=36" alt="Björn Grüning avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/slugger70/" class="contributor-badge contributor-badge-small contributor-slugger70"><img src="https://avatars.githubusercontent.com/slugger70?s=36" alt="Simon Gladman avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/hexylena/" class="contributor-badge contributor-badge-small contributor-hexylena"><img src="https://avatars.githubusercontent.com/hexylena?s=36" alt="Helena Rasche avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/nsoranzo/" class="contributor-badge contributor-badge-small contributor-nsoranzo"><img src="https://avatars.githubusercontent.com/nsoranzo?s=36" alt="Nicola Soranzo avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/abretaud/" class="contributor-badge contributor-badge-small contributor-abretaud"><img src="https://avatars.githubusercontent.com/abretaud?s=36" alt="Anthony Bretaudeau avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/martenson/" class="contributor-badge contributor-badge-small contributor-martenson"><img src="https://avatars.githubusercontent.com/martenson?s=36" alt="Martin Čech avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/eancelet/" class="contributor-badge contributor-badge-small contributor-eancelet"><img src="https://avatars.githubusercontent.com/eancelet?s=36" alt="Estelle Ancelet avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/shiltemann/" class="contributor-badge contributor-badge-small contributor-shiltemann"><img src="https://avatars.githubusercontent.com/shiltemann?s=36" alt="Saskia Hiltemann avatar" width="36" class="avatar" /></a></td>
	</tr>

</table>

</div>

</div>

Tutorial Content is licensed under <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.<br/>